I am having the exact same symptoms! Except my AM stations seem to drop off as well. I have been struggling with it for a couple of weeks now and it seems to be getting worse. I also experienced a signal drift where the station slowly fades away, and after some bumps (I have a very stiff suspension) it seems to get tuned to a different station. When this happens, the station displayed on the empeg remains the same. I recently replaced by HDD with v3 software because my previous HDD stopped spinning up successfully. If I can find a replacement (havn't started looking), I will gladly send mine to you to increase your data points.
_________________________
Ryan here... Empeg [08000462] 40 Gig with Subaru WRX sport wagon attached... (still! pending memory + LED upgrade, sheesh, I've been sitting on my ass for years)