have you done a thorough scan for both viruses and ad-ware recently?
might want to try defragmenting your HD &/or clean the windows registry...
(as far as I know, you should have a program to do this [to clean the registry], don't do it manually)
everything that I know (not much, just a bit of experience from messing around with stuff) is telling me that ftp programs shouldn't be causing windows to crash...