When you are ready to record and you are monitoring the instrument from the DAW, do you hear a clean signal (which is then recorded wrongly) or do you hear the glitching sound (Which is recorded exactly as it is)?
I am talking about monitoring from the DAW as opposed to direct monitoring from the Audio Interface.
I would guess the latter is true, in which case my money would be on a problem in the input chain, as opposed to the OS as you are suggesting. (Also keeping in mind that I’ve never heard of such a problem from anyone else)
The way I would attempt to debug this would be by recording a Clean signal to a new track on a new project. No effects, no amps modelling, no nothing whatsoever. Just the instrument coming through the Audio Interface, straight into an audio track.
If the problem is still there after doing this, I would start replacing elements in the chain.
Changing the Audio Interface is the obvious thing, but I would also attempt to change cables and or USB port on the MBP and attempt to record with a different instrument, or even better with just a vocal microphone. Also eliminate anything extra in the chain, both on the digital side, such as UBS hubs, but also on the audio analog side (Although it sounds as if you have already tried most of this stuff)
EDIT: To be honest though, re-reading your initial post, I am starting to have doubts as you mention the problem disappearing on its own just by upgrading the OS. This is highly unusual am I am now wondering whether there is something else in your software setup that is interfering.
The obvious way to debug that would be to do what Apple themselves would suggest, which is restoring the MBP and OS to factory, do NOT restore from backup, install only your DAW without any additional plugins and/or drivers (or even better just try with GarageBand) and see if the problem is still there.
I’d be gutted if I had to go through all of this, but if nothing else works you might not have any alternative.
Good luck
