OK, after much confusion and idiocy on my part (!) I have my system up and running. Quick overview:
two Mac Pro's
1 8 core 2.4 16 gig ram SL 10.6.6 Pro Tools 9 HD 3 accel
1 4 core 2.66 9 gig ram SL 10.6.6 VEPro 4.1.7553 Apogee Rosetta 800 Ensemble 32 PCIe
All systems run as expected, except I'm getting pops and after looking more closely at the wave files, I think they're actually dropouts. You can see the wave actually broken! Anyway, the pops only appear on the ethernet busses, even if I'm only running 1 stereo track into PT. Now, if I midi from the 8 core to the 4 core, and run all four stereo tracks out of the Rosetta 800 simultaneously, it's clean as a whistle. It has to be about the Ethernet buss. I'm running them direct out of port 2 on both with static IPs and no router using a brand new 4' Cat 6e cable. How can I get rid of these pops and/or dropouts? Tried changing the buffer to 2, but it didn't seem to help. Thoughts anyone?