Latency between audio and keyboard commands (10.9 and 10.10)

Apologies for the length of this. Don't pay too much attention to the precise details of my setup, because we're dealing with practically identical systems, where the problem occurs depending on the version of OSX.
I'm on a 2010 Mac Pro, 2.66GHz 12-core, 32GB RAM. Audio via Firewire into a MOTU UltraLite mk1
Basically, I use a program called Transcribe!, which is for analysing music. You can slow down audio files, loop sections, etc, but most importantly it displays a waveform where you can add markers to show where the beats, measures and sections are (for easier navigation). You do this by tapping on the keyboard... B to enter a beat, etc.
In both Mavericks and Yosemite, something is going wrong.
If I simply play the file, the waveform scrolls by smoothly, and I can see that the "current position" indicator is accurately reflecting what I'm hearing (a big peak for a cymbal crash, etc). But if I then start tapping the beats on the keyboard, the waveform starts to scroll jerkily and the beat markers land about 130 milliseconds late... that's pretty disastrous when you're trying to accurately analyse the music.
Obviously a lot of variables, but here's the weird thing. THIS WORKS PERFECTLY IN MOUNTAIN LION (on the same computer). Everything is on the same computer, with the same peripherals. The only difference is the OSX version and the hard drive it's installed on... but I've tried this on two different drives (one SSD, one HDD) and with both 10.9 and 10.10.
(And another weird thing - I can't recreate the problem on my MBPr. It seems to be restricted to 10.9 and 10.10 on this Mac Pro)
I can't see anything meaningful in Console or Activity Monitor, and my basic System Preferences are all the same. The actual processing of audio and video is fine... this seems to be some kind of issue with keyboard control. Any suggestions gratefully received.

A couple of little possibilities were bugging me.
Works fine on MBP, but not on Mac Pro... could be a dodgy keyboard? Nope, plugged same keyboard into MBP and it's fine.
Could be an actual fault on this particular Mac Pro, that somehow only manifests itself in Mavericks/Yosemite? Nope, plugged in my older (2008) Mac Pro and the same thing happened. Latency with 10.9 and 10.10, but not on earlier versions of OSX.
Really don't get this!

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