It seems that, when using "Synchronize only the following" for auto-synchronization settings, the contents of some directories are always synchronized, regardless of whether or not the files have actually changed.
After a lot of trial-and-error, including wiping all music off my Vision:M

Unfortunately, every directory, with a non-default destination path, gets re-transferred every time I do an auto-sync. I verified this by making two identical copies of a directory containing MP3 files. I set one directory to auto-sync with the default destination. The other directory was configured to use a non-default destination. Autosynching would then always transfer the directory with the non-default destination.
I can give a lot more information, including the (freely redistributable) MP3 files that I used to narrow down this problem. I've tried using the debug version, but DebugView doesn't seem to give any useful information, aside from "Uploading track ...", "Uploading to ...", etc.