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Cubase SX2, Pulsar 2

Recently whenever I record a external midi instrument track to disk, a drum-loop for instance, the track will start recording fine but then there will be a small stutter about 4 beats in, if I leave it running to overdub that part again it will be fine, it's just that 4th beat in, as though something is initializing. Any ideas as to what this could be, many thanks.

I'm not sure what you mean, but try to diminish the midi note that triggers your loop with a few points (high resulution, see Cubase prefs).
You won't hear that very small gap.

Specially the first midi note can cause a trigger problem at start of the second one if you start playing exactly from the zero point of the first bar.
A complicating factor can be the end of the loop, when it has another downbeat at the end of it, exceding the real loop length

Update on this, it seems as though the problem is a fault with any MIDI track. Stuttering to keep up and going out of time, I would have thought that this was more likely to happen with Audio, anyone have any suggestions as to what this might be caused by?

Another update, sorted this problem out after playing about with settings, seems that if under "send midi timecode" and "send midi clock" I choose Creamware midi in/out it messes up the timing. It has always been guesswork for me with these settings so don't know if I should have had these checked in the first place, can anyone shed any light, thanks.

Cheers, but in the end it was because I was using emulated midi. All set up fine now, thanks.