I just found a little quirk, and it seems easy enough for me to fix, but I'll mention it here anyway.

When you are in "Keep remote directory up to date" mode, and there are two remote files that have the same name except different cases (this can only happen in a *nix system), then whenever you make a change to _any_ file locally, your local file with the same name as that remote one (there can only be one file of course in Windows) gets copied every time. It appears, if you wouldn't look at the log, that the one unrelated file you are working on gets uploaded twice.

To fix it, simply delete one of the remote files.