When I start adding files into those bottom folders, it's going to get even worse. The remote FTP site is the problem - it just takes a long time to recursively work through the folders, some 6 layers deep. My short experience with FFS (free version) is that the comparisons can take a long time (I have an empty folder structure that contains 320+ folders, no files) and it takes about 3 minutes to just do a compare (File Time and Size). But the one that I really like is called Fast Backup, and I think FreeFileSync could vastly benefit from this feature.
I use a program called SyncBackPro to back up several of my servers - it has some great features.
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