Actually your problem reminds me of the problem I had with my Empeg MK2a. Well, had...erm, I've never been able to solve it really. Combining the 10gig it came with with a new 48gig IBM resulted in slowdowns when synching and eventually locking up.
I just decided in the end that those two drives didn't get along too well and I removed the 10gig. (strange since they're both IBM)
I'm currently only using the 48gig and I'm awaiting the new IBM 60gig. 60gig should be enough for my needs and then some, so then I can get rid of the 48gig.
Nobody was able to solve my problem (not even Hugo), so I gave up on it.