Just as an update in case anyone else comes across a similar issue - I haven't gotten it totally fixed but it seems to be related to my thermistor settings for my hotend. I was using a config that I found from CNC Kitchen (he swapped a Prusa to Duet) and I am using the same heater/thermistor so I assumed it would work fine. Once I found the datasheet for the thermistor and entered the values from there it seems to be a lot better. I am going through tweaking and PID tuning now but I am relatively confident that with some tuning I can make this defect disappear. Something to look for if you run into the same problem.
Best posts made by mdbergholm
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RE: One issue after swapping from smoothieboard