You said your database rebuilds twice per upload? So are you saying that because the timeout expires waiting for a reboot, that somehow causes a SECOND rebuild to happen? That on-empeg-rebuild should only happen if the original sync failed in the first place. A normall process is: upload changes, jEmplode requests database rebuild (you should see the rebuild status in jEmplode), jEmplode reboots player, player reboots (and does not rebuild), player finishes loading, jEmplode reconnects to player, done.

The timeout should happen if it goes like this:
upload changes, jEmplode requests database rebuild, rebuild fails, Empeg reboots and rebuilds itself, jEmplode waits and times out.

I'm not sure where the second reboot or rebuild would happen in this process or for that matter why your Empeg would be rebuilding itself. Are there any error messages that jEmplode displays? Can you run a full sync and send me the console output from that? (also, if you would, turn off serial/usb so those exceptions don't get all mixed up with the other debug info in the logs).

ms