I have a Toshiba laptop, running Windows 7 Basic.
Everything was working fine, then all of a sudden my applications started behaving strangely.
If I had anything running in FULL screen mode it would minimise after a few minutes (VLC media player, windows media player and games)
When playing games, not in full screen mode, the game would suddenly pause as if you had clicked away.
And now I cant get my Vodafone software for my 3G to open correctly. It keeps looping and does not open all the way.

I know that this sounds LIKE a virus, I've run full scans using Kaspersky and Malwarebytes and they both report 0 THREATS.
Any advise is more than welcome. Do a clean boot. See if the problem persists.

http://support.microsoft.com/kb/331796

If the problem doesn't happen in the clean boot state, start enabling items until you find the culprit. Here are complete instructions on doing what is suggested above:

Open msconfig and on the General tab choose "selective startup" (uncheck all three items) and reboot. Does the problem still occur? If not, start adding items back to msconfig one or two at a time, rebooting after each change, until the problem reappears and you'll have identified the offending process. This is clearly a time consuming procedure, but it is the best way to DETERMINE if some process loading with the system is the CAUSE of your problem.

After you've isolated the cause, do not use msconfig to permanently disable the process. Instead, if it is a service go to START - RUN and type: services.msc (then press enter) and disable the service OR, if it a program, you can download & run a simple app such as Mike Lin's Startup Control Panel (http://www.mlin.net/StartupCPL.shtml) to enable, disable, or otherwise manage startup programs.
Thanks guys for the advice! I will try it and report back.