To start with, Internet Explorer isn't the same as Windows Explorer. And I'm sure you run the last, because it's the program that shows your desktop.

Taking off Internet Explorer is a bad idea. It's an integral part of the OS. Just not running it is a much better idea. Why did you "take it off" and how did you do that?

If the problem didn't appear before you got that trojan, it seems it's related. If it appeared already before yesterday, it's not related. I don't know. You do.

My suggestion: see if you can download IE 8 for Windows 7 from Microsoft to reinstall it. But I don't think you can. Then do a repair install of your OS from the Windows 7 DVD.
Or take the plunge and install the Internet Explorer 9 beta.

Kees

Kees