So I installed Firebug, and took a look at the code. It seems like the data has the correct format. Now, I am wondering if I have done some of the 'require' incorrectly.

This is what I see on Firebug:

require(["dojox/charting/Chart", "dojox/charting/StoreSeries", "dojo/store/Memory", "dojo/store/Observable",
"dojox/charting/axis2d/Default", "dojox/charting/plot2d/StackedBars", "dojox/charting/plot2d/Markers", "dojo/ready"],
function(Chart, Default, StoreSeries, Memory, Observable, StackedBars, Markers, ready){
ready(function(){
var dataEnrolled = [{"y":"5","text":0,"stroke":"black","tooltip":0},{"y":"10","text":1,"stroke":"black","tooltip":1},{"y":"7","text":2,"stroke":"black","tooltip":2},{"y":"23","text":3,"stroke":"black","tooltip":3}];
var dataExpected = [{"y":"20","text":0,"stroke":"black","tooltip":0},{"y":"50","text":1,"stroke":"black","tooltip":1},{"y":"14","text":2,"stroke":"black","tooltip":2},{"y":"100","text":3,"stroke":"black","tooltip":3}];
//alert(dataEnrolled).toSource();
var chart = new Chart("simplechart", {
title: "Participants (Enrolled X Expected)",
titlePos: "top",
titleGap: 25,
titleFont: "normal normal normal 20pt Tahoma",
titleFontColor: "black"
});
chart.addAxis("x", {stroke:"black",font:"normal normal bold 12pt Tahoma"});
chart.addAxis("y", {stroke:"black", font:"normal normal bold 12pt Tahoma", vertical: true, labels:[{value:0, text:""}, {value:1, text:"INCA"}, {value:2, text:"AC"}], rotation:20});
chart.addPlot("default", {type: "StackedBars", markers:true, gap:5});
//chart.addSeries("Series A", <br />
<font size='1'><table class='xdebug-error xe-notice' dir='ltr' border='1' cellspacing='0' cellpadding='1'>
<tr><th align='left' bgcolor='#f57900' colspan="5"><span style='background-color: #cc0000; color: #fce94f; font-size: x-large;'>( ! )</span> Notice: Undefined variable: enrolled_array in C:\wamp\www\recipe\dojoTesting\barsite2.php on line <i>76</i></th></tr>
<tr><th align='left' bgcolor='#e9b96e' colspan='5'>Call Stack</th></tr>
<tr><th align='center' bgcolor='#eeeeec'>#</th><th align='left' bgcolor='#eeeeec'>Time</th><th align='left' bgcolor='#eeeeec'>Memory</th><th align='left' bgcolor='#eeeeec'>Function</th><th align='left' bgcolor='#eeeeec'>Location</th></tr>
<tr><td bgcolor='#eeeeec' align='center'>1</td><td bgcolor='#eeeeec' align='center'>0.0654</td><td bgcolor='#eeeeec' align='right'>382456</td><td bgcolor='#eeeeec'>{main}( )</td><td title='C:\wamp\www\recipe\dojoTesting\barsite2.php' bgcolor='#eeeeec'>..\barsite2.php<b>:</b>0</td></tr>
</table></font>
<br />
<font size='1'><table class='xdebug-error xe-warning' dir='ltr' border='1' cellspacing='0' cellpadding='1'>
<tr><th align='left' bgcolor='#f57900' colspan="5"><span style='background-color: #cc0000; color: #fce94f; font-size: x-large;'>( ! )</span> Warning: Invalid argument supplied for foreach() in C:\wamp\www\recipe\dojoTesting\barsite2.php on line <i>35</i></th></tr>
<tr><th align='left' bgcolor='#e9b96e' colspan='5'>Call Stack</th></tr>
<tr><th align='center' bgcolor='#eeeeec'>#</th><th align='left' bgcolor='#eeeeec'>Time</th><th align='left' bgcolor='#eeeeec'>Memory</th><th align='left' bgcolor='#eeeeec'>Function</th><th align='left' bgcolor='#eeeeec'>Location</th></tr>
<tr><td bgcolor='#eeeeec' align='center'>1</td><td bgcolor='#eeeeec' align='center'>0.0654</td><td bgcolor='#eeeeec' align='right'>382456</td><td bgcolor='#eeeeec'>{main}( )</td><td title='C:\wamp\www\recipe\dojoTesting\barsite2.php' bgcolor='#eeeeec'>..\barsite2.php<b>:</b>0</td></tr>
<tr><td bgcolor='#eeeeec' align='center'>2</td><td bgcolor='#eeeeec' align='center'>0.0687</td><td bgcolor='#eeeeec' align='right'>393168</td><td bgcolor='#eeeeec'>array_to_chart_json( )</td><td title='C:\wamp\www\recipe\dojoTesting\barsite2.php' bgcolor='#eeeeec'>..\barsite2.php<b>:</b>76</td></tr>
</table></font>
[]);
//chart.addSeries("Series B", <br />
<font size='1'><table class='xdebug-error xe-notice' dir='ltr' border='1' cellspacing='0' cellpadding='1'>
<tr><th align='left' bgcolor='#f57900' colspan="5"><span style='background-color: #cc0000; color: #fce94f; font-size: x-large;'>( ! )</span> Notice: Undefined variable: expected_array in C:\wamp\www\recipe\dojoTesting\barsite2.php on line <i>77</i></th></tr>
<tr><th align='left' bgcolor='#e9b96e' colspan='5'>Call Stack</th></tr>
<tr><th align='center' bgcolor='#eeeeec'>#</th><th align='left' bgcolor='#eeeeec'>Time</th><th align='left' bgcolor='#eeeeec'>Memory</th><th align='left' bgcolor='#eeeeec'>Function</th><th align='left' bgcolor='#eeeeec'>Location</th></tr>
<tr><td bgcolor='#eeeeec' align='center'>1</td><td bgcolor='#eeeeec' align='center'>0.0654</td><td bgcolor='#eeeeec' align='right'>382456</td><td bgcolor='#eeeeec'>{main}( )</td><td title='C:\wamp\www\recipe\dojoTesting\barsite2.php' bgcolor='#eeeeec'>..\barsite2.php<b>:</b>0</td></tr>
</table></font>
<br />
<font size='1'><table class='xdebug-error xe-warning' dir='ltr' border='1' cellspacing='0' cellpadding='1'>
<tr><th align='left' bgcolor='#f57900' colspan="5"><span style='background-color: #cc0000; color: #fce94f; font-size: x-large;'>( ! )</span> Warning: Invalid argument supplied for foreach() in C:\wamp\www\recipe\dojoTesting\barsite2.php on line <i>35</i></th></tr>
<tr><th align='left' bgcolor='#e9b96e' colspan='5'>Call Stack</th></tr>
<tr><th align='center' bgcolor='#eeeeec'>#</th><th align='left' bgcolor='#eeeeec'>Time</th><th align='left' bgcolor='#eeeeec'>Memory</th><th align='left' bgcolor='#eeeeec'>Function</th><th align='left' bgcolor='#eeeeec'>Location</th></tr>
<tr><td bgcolor='#eeeeec' align='center'>1</td><td bgcolor='#eeeeec' align='center'>0.0654</td><td bgcolor='#eeeeec' align='right'>382456</td><td bgcolor='#eeeeec'>{main}( )</td><td title='C:\wamp\www\recipe\dojoTesting\barsite2.php' bgcolor='#eeeeec'>..\barsite2.php<b>:</b>0</td></tr>
<tr><td bgcolor='#eeeeec' align='center'>2</td><td bgcolor='#eeeeec' align='center'>0.0689</td><td bgcolor='#eeeeec' align='right'>393168</td><td bgcolor='#eeeeec'>array_to_chart_json( )</td><td title='C:\wamp\www\recipe\dojoTesting\barsite2.php' bgcolor='#eeeeec'>..\barsite2.php<b>:</b>77</td></tr>
</table></font>
[]);
//chart.addSeries("Series A", [{"y":"5","text":0,"stroke":"black","tooltip":0},{"y":"10","text":1,"stroke":"black","tooltip":1},{"y":"7","text":2,"stroke":"black","tooltip":2},{"y":"23","text":3,"stroke":"black","tooltip":3}]);
//chart.addSeries("Series B", [{"y":"20","text":0,"stroke":"black","tooltip":0},{"y":"50","text":1,"stroke":"black","tooltip":1},{"y":"14","text":2,"stroke":"black","tooltip":2},{"y":"100","text":3,"stroke":"black","tooltip":3}]);
chart.addSeries("Series A", dataEnrolled);
chart.addSeries("Series B", dataExpected);
chart.render();
});
}); 

Great, I got the bar working :)
But I still have some questions, if you don't mind me. I know you are probably tired of me at this point.

Questions:
1. I wanted to create a StackedBar, the result is correct but I am not using the StackedBar, you see it in the code, I am using regular Bar. When I tried to use StackedBar the graph does not show. How can I fix that?
2. I was able to add the SelectableLegend, so it can be a little fancy, and I also added Tooltip. However, for the tooltip only the Uruguay Bar is able to show the correct array value. For the other bars, it seems like its getting the array index and not the value. How can I change that so it can correcly display the value when I hove over the bar?

Thanks again for all your help.

<!DOCTYPE html>
<html >
<head>
<?php
//connect to database
$con = mysql_connect("localhost", "test", "test") or die('Sorry, could not connect to database server');
mysql_select_db("brazil", $con) or die('Sorry, could not connect to database');

//array of participants enrolled
$array1 = array();
$query1 = "SELECT participantsEnrolled from inca UNION (Select participantsEnrolled from ac)";
$result = mysql_query($query1) or die ('Could not find cities');

while ($enrolled = mysql_fetch_array($result, MYSQL_BOTH)){
    $array1[]=$enrolled['participantsEnrolled'];
    }
    $array1 = array_map('trim', $array1);
    print_r($array1);

//array of participants expected
$array2 = array();
$query2 = "SELECT participantsExpected from inca UNION (Select participantsExpected from ac)";
$result2 = mysql_query($query2) or die ('Could not find cities');

while ($expected = mysql_fetch_array($result2, MYSQL_BOTH)){
    $array2[]=$expected['participantsExpected'];
    }
    $array2 = array_map('trim', $array2);   
    print_r($array2);

function array_to_chart_json($array) {
        $toReturn = array();
        foreach ($array as $key=>$value) {
            $toReturn[] = array(
                'y'=>$value,
                'text'=>$key,
                'stroke'=>'black',
                'tooltip'=>$key
            );
        }
        return json_encode($toReturn);
    }
?>

<link rel="stylesheet" type="text/css" href="../dijit/themes/claro/claro.css" />

<script>dojoConfig = {parseOnLoad: true}</script>
<script src="//ajax.googleapis.com/ajax/libs/dojo/1.8.1/dojo/dojo.js" 
                data-dojo-config="async: true"></script>

<script>require(["dojox/charting/action2d/Magnify", "dojox/charting/action2d/Tooltip", "dojox/charting/widget/SelectableLegend", "dojox/charting/Chart", "dojox/charting/axis2d/Default", "dojox/charting/plot2d/Bars", "dojox/charting/plot2d/Markers", "dojo/ready"],
   function(Highlight, Tooltip, SelectableLegend, Chart, Default, Bars, Markers, ready){
   ready(function(){

    var dataEnrolled = <?php echo array_to_chart_json($array1); ?>;
    var dataExpected = <?php echo array_to_chart_json($array2); ?>;
    //alert(dataEnrolled);
    //alert(dataExpected);

    //alert(dataEnrolled).toSource();



    var chart = new Chart("simplechart", {
      title: "Participants (Enrolled X Expected)",
      titlePos: "top",
      //displayRange: 700;
      titleGap: 25,
      titleFont: "normal normal normal 20pt Tahoma",
      titleFontColor: "black"
    });

    chart.addAxis("x", {stroke:"black",font:"normal normal bold 12pt Tahoma", min:0});
    chart.addAxis("y", {stroke:"black", font:"normal normal bold 12pt Tahoma", vertical: true, labels:[ {value:0, text:""},{value:1, text:"Uruguay"}, {value:2, text:"Mexico-Sonora"},{value:3, text:"Mexico-Guadalajara"}, {value:4, text:"Chile"}], rotation:20});
    chart.addPlot("default", {type: "Bars", markers:true, gap:5});
    //chart.addSeries("Series A", <?php echo array_to_chart_json($array1); ?>);
    //chart.addSeries("Series B", <?php echo array_to_chart_json($array2); ?>);
    chart.addSeries("Participants Enrolled", dataEnrolled, {fill:"blue"});
    chart.addSeries("Participants Expected", dataExpected, {fill:"lightblue"});

    var mag = new dojox.charting.action2d.Highlight(chart,"default");
    //var anima = new dojox.charting.action2d.Tooltip(chart, "default");
    new Tooltip(chart, "default");

    chart.render(); 
    var selectableLegend = new dojox.charting.widget.SelectableLegend({chart: chart, outline: true}, "selectableLegend");

  });
});
</script>
</head>
<body class="Wetland">
    <div id="simplechart" style="width: 600px; height: 500px; margin: 10px auto 10px auto;"></div>
    <div id="selectableLegend"></div>
        </body>
</html>