Please enable session logging and once the problem occurs, attach a respective log here. Also attach a log showing correct upload (for comparison).
I can't seem to pin it down, and it seems pretty random, but every now and then when I edit a file via WinSCP it changes the permissions on the file when it's re-uploaded. This can have disastrous consequences when you're dealing with CGI scripts, etc. I can't find any options or settings that would cause this. Is there a known bug re: this or am I missing something somewhere? At least once a week I will edit a file, WinSCP will re-upload it and the permissions get changed from 755 to 644 which makes CGI scripts not execute any more.