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Yeah but that's quite a short print. Usually when it happens on mine it's after more than one hour. Even had it go up to three hours before it happened (it also depends on the print and how many times it needs to retract the filament it seems). Then, as you said, it's quite possible that the bowden MMU setup with its different retraction settings has something to do with it.
The clog always happens just below the ptfe tube in the hotend.

Setup picture attached. The blue thing on the left hand side is the temperature sensor.
Lot's of cables :)