You could try the debian version (2.3.2) to see whether there's any difference.
My experience with the debian version is that it locks up when transferring/comparing huge numbers of tunes (>14000 in my case).

Of course, the problem you are seeing might also be caused by cygwin's rsync.
For testing, it would be nice to have a replacement for that too.

I'd be interested to see what you have found out. Now's the time to shut down my computers and leave for the airport.

Pim