When I start up the computer, the Desktop and taskbar go away after 20 secs and do not come back. I can access things through task manager (which is how I got here). I've swept with Trend Micro and it quarantined some files but to no avail. I've looked up the problem, and have even see some threads on this forum and nothing has worked. First of, any advice?

If all else fails, I'm thinking about reinstalling windows, but I need to save some files first. I have a question, will the files I save on a website or a disc be infected with the virus that is most likely caused this?

If you've been attacked, the damage is already done.

The non-exe files that might be corrupted are:
- Anything capable of executing a macro (Office files, e.g.)
- Any Active control that you downloaded

Files you save on a website are vulnerable to attack on that website. They should be passed through Spybot, AVG or McAfee (or Trend) before you try to use them.

My advice is thus to reinstall your system (but with a proper format of your HDD) and go from there.

I installed ComboFix and let it do it's thing. now the desktop and taskbar stay up, problem fixed.