about external hard drives

I'm in the process of trying to get rid of an infection, for now I'm considering just reinstalling the Win 7, which whipes the drive but....If I have all my documents on an external flash drive...won't it be infected too? If I hook it back up to a fresh PC won't it just get reinfected? ( I know I'm infected but Avast didn't catch it and a malware bytes scan didn't catch it either.)

 

Symptoms are , Avast is disabled, isn't loading at a start up, once it shows up a few minutes later the avast windows says it's not on and when I press 'start' a window comes up asking if "I want to alow this program to makes changes to this computer", which isn't normal for Avast.

+I can't get into Safe Mode.

Will include this link to the CNET page I got it from

http://download.cnet.com/Free-Audio-Converter/3000-2140_4-10893961.html

I downloaded it without checking all the comments, but it's just so you can see that even if the Avast can't find it...somethings there.

Never trusting CNET again!!

 

Here are the log results from my scans. I'm not sure what's significant or safe to remove. Rougue Killer found no 'bad processes' but some 'registry' and 'Anti-rootkit ' entries. Hitman found three things also...logs attached.

The original post was just about, before I was about to try fix things myself by reinstalling windows, wondering if I could just get reinfected by the external hard drive I backed up my files to. I thought this would be the place to check that.

But now I'm going through the RUN&READ ME link you sent.