This has got me puzzled pretty good. Weird problem you have here. It is almost as if, somehow your "Virtual C" from your previous softmod is still being loaded but I wouldn't think so.
I would try turning off any firewalls you may have running while ftp'ing to the xbox.
You could also try using a jump/key drive to transfer an ini file to the xbox HD to see if it becomes corrupted that way.
Another idea you can try is alternating the dashboard that is running when you ftp into the xbox, like ftp with evox running as the dash, zap a file over, and if corrupt, boot to unleashX and try again, Just to rattle off a few things off the top of my head that I would try in your spot.
For the most part, your problem doesn't sound TSOP related. It may just be coincidence that it is happening on your first (or latest) attempt.
Hope this helps, and be sure to let us know if you get the problem figured out.