Had this problem with 42-pre5, so I upgraded to 42.

I set a wendy flag on one song, and make no other changes, then sync.

The status indicator bar window pops up, says "Locking Player Interface", then nothing. JEmplode no longer refreshes the screen, either. The player eventually gives up, per the serial port output:
server_protocol_handler.cpp:1383:Timeout during synchronise, restarting player

And in fact I then have to resynchronize to get a useful database...

I figure I'm going to have to look at this, but I was wondering if anyone had ideas. I think I'm going to sleep now.