Your problem sounds a LOT like the problem I was having. I lived with it for about a year, thinking it was a power issue with my car's alternator.
Only when attempting to upgrade the drive did I relaize the problem was with the first connector on the drive cable. So, instead of running two drives in there, I just ended up running the new bigger drive on the previously unused connector on the cable.
I sent an email to support asking about purchasing a replacement cable and haven't received a reply, but I'm not in any big rush since I know have a perfectly working Empeg again, and with more storage than I had before.
SO, switch the connectors and see if that fixes your issues. Very simple and quick to do, so it will be worth it. You just won't be able to easily copy songs from on old drive to a knew one while you're in there.
Scott