I find this particular line very curious...

server_protocol_handler.cpp:1386:Timeout during synchronise, restarting player
[21] player: old system call.


It seems almost as if you had a mismatch between the emplode version and the player version. The boot of the player looks like 2.0 though. Please double check the driver installation for (possibly even reinstall) the USB driver set, per Tony's message above. It looks like it is timing out on a protocol message...

Another thought, after the fsck, is to manually allow the databases to rebuild on the player first. This should not matter, but it would not hurt anything.

Lastly, just for kicks, enable sync via the serial port and try to sync that way. Obviously you do not want to send any files up, but you might be able to just "touch" a playlist or something and force the sync. It would be a good test to eliminate the protocol and player versions vs. ethernet or USB issues.