Just now I had loads of pops and crackles through my empeg. I knew it wasn't a bad rip or anything like that as I've listened to this album before and I made sure it was okay when I encoded it. Also it would reappear in a different place if I flushed the music cache by seeking forward a few times and then going back to the original track.
Looked at the kernel ring buffer and there were huge numbers of errors about the HD and not being able to read sectors.
So... knowing that everybody has had loads of problems with the HD cable and since it's actually a FAQ I opened up the empeg. Recrimped the HD cable and now it's fine... (cross fingers)

I guess it's time for me to get a replacement cable from Rob.

If anybody else has lots of pops when playing a known good track then check your cable!

- Trevor