To control the size of primary and secondary IE windows, close all IE windows. Launch webpage in Internet Explorer, right-click some weblink, and choose Open in New Window. Size the secondary window the way you want your windows to be, then close it by clicking on the X icon in the top-right corner while holding down the Shift key. Repeat this for the primary window that remains. You may have to repeat the process at times.
However, If you always want your webpage to open in precisely with the same size and position, you can add a JavaScript to the main page URL. Select Internet Options from the Tools menu and edit the Address line in the Home Page panel so it looks something like this: javascript:resizeTo(750,400); moveTo(0,0);document.location.href='http://www.yourwebsite.com'.
Maybe just a workaround for a time being...?