I've been through everything such as Doug Knox's file association fixes for both .EXEs and .LNK files. Ironically enough, it is seemingly infectous in my household that I was in the process of fixing a clients computer that had lost ALL .exe and .lnk association to the point I had to open Internet Explorer through a Windows folder and go onto the net that way. I've also been through all of the previous documentation and forum posts on this site to no avail.
All icons either linking to an .EXE (.lnk files) or .EXE files themselves show up as generic files and ask "What program do you want to open this with?" such and such. I ran Doug Knox's .LNK and .EXE fixes (http://www.dougknox.com/xp/file_assoc.htm) by choosing C:/Windows/regedit to open the .REG files. This worked, but maybe for about 10 minutes max. After 10 minutes, it would automatically revert back to generic files and not allow executables to be run. Going through all of the information on Google and having absolutely nothing pinpoint the problem or fix the problem, I decided just to backup what I could and do a format and reinstall.
Now, here's where the weird stuff comes in. The computer that has the problem is going through DOS Windows install, so I take my laptop downstairs and plug it into my router and run Ad-aware Professional. It finds 45 or some odd amount of files and I clear them from the system. After I do this, the laptop loses it's file association too! Mind you, the laptop runs on Windows 98 and the computer I am fixing for the exact same problem is running Windows XP Professional.
I'm guessing that Ad-aware either deletes something hazardous which then triggers something else, or the deleted file, to do some loopy stuff and lose file association. Either that or it deletes something vital and makes this problem occur, because the owner of the computer I am fixing also runs Ad-aware and said that she had a bunch of stuff pop up on Ad-watch just prior to the problem starting.
I'm thinking this might become a pretty big problem on a lot of systems running Ad-aware unless someone figures this stuff out, because I've exhausted my options. If you guys need any more information I'll try and provide it.