Sound cuts out at intervals after upgrade to 9.1.6

I applied the 9.1.6 software update to Logic pro today. Started a new project and have just a couple of tracks of Kontakt software instruments in play.
When recording or playing back audio output will stop completely for a few seconds (5 or more) and then comes back (occaisionally with an error message about sample rates mismatch).
I'm using an Edirol FA-101 set to 44.1khz and the project is in 44.1khz. It's a Mac Pro 8 core on latest version of 10.6
everything had been running fairly smoothly before the update - certainly no problems like this - and there have been no changes to the system other than the update.
I've done several restarts of computer, inteface, logic etc. but can't get rid of this. Driving me mad.
Any suggestions?

I know about the mixed case issue. Luckily we only use uppercase. The second case regarding the recompile is a valid, but not applicable in our case.
We are seeing these errors (it appears randomly [to us]) AT RUN-TIME! These objects are there [valid and being executed by many], and one-time it will work and the next maybe, maybe not.
It really makes no sense.
Anybody got any other ideas?
Thanks,
Jason

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