If it’s fine with PLA then my money is on profile issue. Use your PLA profile, and just change the temperature. If that works okay, start tuning for PETG from that point. And delete the old PETG settings.
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I did some more testing, also with different slicers, and it seems to not actually be a PETG specific issue, but rather a model/speed issue. I can get it running without stops if I just reduce print speed. When I set speed to 100% I start getting these weird 10-20 second long stops.
So now in thinking it's the controller locking up because it's overloaded by too many small movmeent gcode commands in rapid succession?