Hm...... a database of 70gigs of music is filling the MKII ram, but Paul's database of 160gig isn't filling the MKIIa ram?

Well, that is the suspected cause. Still unproven. Just a theory.

So that few meg ram difference DOES matter?

The memory does help quite a bit.

Or are Paul's drives spun up all the time? And is his player overheating because of it?

Not that I know of, on both counts.

And to reply to an earlier post in the thread re: flac and alternative file types: Would it keep the drives spun up to play FLAC or WAV? I'm assuming yes because it's a bit hard to cache an 80 meg song in 16 meg ram.

Exactly. Since you need more data per second, you cannot effectively cache that kind of file as easily. Or perhaps, you can cache it, but you burn through it so quickly that it really doesn't help.