Hi again... Hmm - had a listen, and the smallest buffer size is the worst, but then it's starts to be kinda similar (only listened on phone sorry)...
Is it ONLY on the way in, or playback as well?
If u have enough ram, then it's sound like clocking (or digital locking) issue as u said... Having it as the master should be right... Clocking (and buffers etc) would affect playback though too, so the above question counts...
Hmmm was hoping the buffer was the issue - not sure if I can help!
It might be time to send presonus a tech support email!
[edit: yes Matt - I see -- my bad, but just trying to help

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[[double edit: actually - so your FireWire port is fried?? Hmm... Do u have any other reasonably intense units u can test your USB port on? Maybe it's dead / dying too (USB keyboard perhaps)..... If your FireWire died, maybe your whole computer is on the way out??!! :-O]]