Thanks for your report. Though, it works for me.
I have sent you an email with a debug version of WinSCP to the address you have used to register on this forum.
The problem seems to occur when I'm comparing a directory, but not when I'm comparing an individual file. In other words, if I compare an individual file, and copy differences from local to remote, the changes end up on the remote end (after WinSCP shows an overwrite confirmation dialog). If I compare the folder that contains the changed file, and copy the differences from local to remote, the changes do NOT end up on the remote end (there's also no WinSCP overwrite confirmation dialog).
I'm working with the debug version to create a simple test case that demonstrates the problem.