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I recently updated to the Micro Swiss MK10 as well, and I had a few jams to start. I discovered I had been running the temperature far too high. (240+ C) I had done this with the stock hot end because the extruder was having trouble pushing the filament through, and this seemed to be the general suggestion. However, I pushed it too far and clogged my original hot end. When I first replaced it with the Micro Swiss, I was getting similar clogs. I ended up dialing the temperature back down to 210C for most prints. I'm running Hatchbox filament through this at 0.15mm layer height and am now getting some of the best prints I have ever generated from my printer. So I can suggest two things to check - print temperature and filament selection. Good luck and hope you can get your system running smoothly again.