You need to have your flash drive scanned at the same time you clean the infected computer you're working on. There's also a flash drive cleaning program, and I'll post the program for that below, however, please note that it's not fully reliable or always effective. You may need to reformat your flash drive. If you need to use an external medium for transferring the installation programs for antimalware programs, then use a read only cd and download the programs only from recommended download sites.
It sounds like you have a lot of infections and they are of the type that can be cleaned out of your computer, so to begin with, please go through the instructions in This Topic
and make a note of what works and what doesn't. When you finish with that, post in the HijackThis and Malware Removal Forum so they can help you get any remaining files out of your computer which may be left over. The problem with many viruses, is that they leave some files behind to get themselves started back up, and these need to be identified and removed manually. That's why the first steps should help you get your computer back into a working order, but the final steps require that someone knowledgeable help you at the end.
I see chewy posted the link for the flash drive utility in your other thread.
Edited by Zllio, 17 November 2008 - 06:18 AM.