I've had a similar problem.
After a number of retries at resyncing with Emplode it eventually fixed itself.
I connected to the unit with the USB and monitored the situation over the serial and a terminal emulator.
Although if you are having problems using USB then this will not be possible for you.

I've found the support offered by Empeg to be faultless.
They have a fast turnround on fixing the units (I stuck in my own HD and knocked a component on the board which eventually failed) and they had it back to me less than 48 hours after I posted it down to them.
The emails are quick and responsive (apart from the odd one where Mike has mailed me the wrong files :-) but he quickly sent a replacement)
Even when they have all been having fun in the US at the trade shows, they have offered and provided support (including new kernels and player software)

So when is Hugo going to be on Tomorrows World with Phillipa Forester?