ive just been struggling with possibly a similar issue to this after my sync gen just rocked up a couple of days ago.
the issue i was having was that i wanted to use scene mode in ableton to be able to record loops from MD and A4 on the fly. but even though the sync clock was perfectly tight with the the ableton clock when using direct monitoring (ie listening to MD and A4 from soundcard pre-ableton). ableton was still recording some latency in the loops.
solution that is working best for me now is:
-ensure ‘monitor’ is off in the ableton tracks recording signal
-use an ableton track to sample the sync gen pulse (with no track delay in the sync gen software) - so a perfectly aligned sample of the pulse.)
-then adjust abletons track delay to negative whatever until loops are recording perfectly in sync.
the 2 key factors here are:
-having the monitor set to off means ableton will slide track to match track delay offset - it doesnt do this if you have monitoring to ‘in’ or ‘auto’. note that with this method you need to have a soundcard that allows direct monitoring which i think OP does (i have rme ufx)
-and the reason i sample the pulse instead of use the sync gen software is that i find when using ableton scene mode it responds to its own native track delay better. i find the sync gen software will compress the timing between first and second beat to adjust for the track delay, while ableton track delay will offset from the start. also chopping, warping and gating the pulse signal can lead to some killer breakbeat splicing effects… so in this case ableton + sync gen is an epic combo.
not sure its the same issue you have been having, but might help