Just in case anyone was remotely interested in this, I found the problem in the end wasn't MIDI clock but was instead the length of the notes the SPD spits out (too short).
You can gate these in the SPD to make them longer but this has the unfortunate (and inexplicable) by-product of turning off the audio out on the SPD, which is ridiculous.
What I've done instead to solve the problem is:
SPD input channel FX:
pizMIDI converter3 - filter out all note off messages
JS Fixed Note Length v0.3 - set note length to 1/16 (they're just triggering one-shot samples so it doesn't matter)
That way you end up with much longer notes with proper note on and off messages and everything works nicely.
Thanks again for help though...
J
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