Mysterious clicks when recording audio.

Just the odd click and pop that should not be there. What are the possible causes? I have the highest spec iMac I could get (January 2013) so I'm suprised this is happening.

Recording delay should be set to zero unless you're done the loopback test and it's required to get the timing correct. Record Delay is to compensate for audio drivers that don't correctly report timing/location information to that system. However, that should cause the clicks you're experiencing.
Would you try the I/O buffer at 64 or 128 and see if it changes the click situation, I know you said it was set to 1024 but that's not a good test.
Are you using any other digital equipment with the M/Box, s/pdif...etc
My only comment regarding Avid is they make pretty bad core audio drivers, you can never run them reliably with the same settings you would use on drivers from MOTU or RME. That said, don't seem like you should be getting noise with a new system, so... no, I'm sure it's not the processor struggling. 

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