I had a brief look at your patch, nothing jumped out as obviously wrong. The only thing I did notice is you're using a lot of dials with red outputs. I'm only guessing but I think these might use more processing than a standard 'dial p' with a blue output. I also tend to use midi in objects rather than the cc drop down to assign controls, though I doubt that's the cause. I have no idea if these things have anything to do with your issue.
What's your clock source? I've had trouble with getting clock out of my laptop(ableton)... Not just for axoloti, It works fine with some gear, and not with others (My work around is to have a clip in Ableton that sends out the same note every 16th and send that to the axoloti, then use the note gate input as a 4ppq clock, works fine...).
If you can, try syncing to something else that sends clock and see if that's any better?
I also get problems if I have Ableton and the patcher running at the same time, just something to be aware of.