On my MkII:
Track 3 set to Dual VCO, Track 4 set to CP Classic.
Track 3 produces a short click sound on the first trigger after its choke group partner track 4 (CP) has sounded. Subsequent triggering of sound 3 are as expected (no click) until after sound 4 is next triggered.
Most noticeable if you have a sound on track 3 with a longer attack like a synth sound.
It doesn’t seem to matter how long you leave it after sound 4 has played before triggering sound 3 - the click is there on the first press or trigger from the sequencer.
If you swap the sounds (3 = CP, 4 = Dual VCO) you get the same result, reversed: click on pad 4.
The click only seems to be present if sound 3 is set to Dual VCO and sound 4 is set to CP but it is still present if the level of the analog machines are set to zero level.
Other machine choices (including the other SY sounds) don’t produce the click as far as I can tell.
This doesn’t seem to be an issue on the other choke grouped pairs of 7/8 and 11/12 - it’s just the combination of Dual VCO and CP in the 3/4 choke group.