On my desktop, I all of a sudden have a little blue rectangle with two white squares in it filling up half of the square. Occasionally the squares are changing color. The rectangle is only about 1/16 of an inch big. It can be moved around on the screen. There is nothing running on startup when doing msconfig. I have ran malwarebytes and symantec and nothing is working.

Anyone have an idea of what type of virus this may be or how to fix it?

We have no way of knowing for sure unless you post some logs, one of which should be the MBA-M scan log and also a HiJackThis log.

As jholland1964 said, Run MBA-M and Hijackthis, here are some instructions for them

1. - Download Malwarebytes' Anti-Malware (http://www.download.com/Malwarebytes...=dl&tag=button) to your desktop.

* Double-click mbam-setup.exe and follow the prompts to install the program.
* At the end, be sure to checkmark the Update Malwarebytes' Anti-Malware and Launch Malwarebytes' Anti-Malware, then click Finish.
* If an update is found, it will download and install the latest version.
* Once the program has loaded, select Perform full scan, then click Scan.
* When the scan is complete, click OK, then Show Results to view the results.
* Be sure that everything is checked, and click Remove Selected.
* When completed, a log will open in Notepad.
* Post the log back here.

Make sure that you restart the computer.

The log can also be found here:
C:\Documents and Settings\Username\Application Data\Malwarebytes\Malwarebytes' Anti-Malware\Logs\log-date.txt
Or at C:\Program Files\Malwarebytes' Anti-Malware\Logs\log-date.txt

2. - Download hijackthis and post the log.

In your reply, post the logs (in this order):
1. - Malware Bytes Log
2. - Hijackthis Log

Thanks,

Cohen