Security System Warning pop-up

I'm really not sure what is going on with my system. I've suddenly started getting these pop up windows titled Security System Warning. I also have the little yellow triangle popping up in my taskbar telling me my computer is in danger...blah, blah, blah. I've disabled Windows Messenger to get rid of that. At the same time, I'm also getting occasional windows opening in Firefox and IE as various pop up ads. I've run Spybot and Virtumonde comes up as a problem. I have Spybot fix it. I run Spybot again, it's still there. I've run VundoFix and it says that it hasn't found any infected files.
Also, when my computer starts up I get a box saying that Windows cannot open the file command.com. I just cancel it, and it starts right up. Is that part of the problem as well? I also cannot run any commands. I've tried running regedit, but I get the same message that Windows cannot open the file. However, when I type in regedit.exe it opens right up. I'm really at a loss. What can I do?