I adjusted the program using the recommendations in the documentation, but now something strange is going on. It seems to be copying over all the files that it had already copied. I have thousands of differential backup sets and winscp seems to start at the beginning every time I run it. Synchronizations are now taking forever.
They're both Windows machines, and I've checked the timestamps and they're the same on both ends as far as I can tell (even when viewed via FTP). Since this happened so recently, I suspect the recent DST change March 11th, but I really don't know how to proceed from here.