I suspect an electrical issue on the motherboard.
- What happens if you swap the bed and hotend thermistor, and/or plug one of your reference thermistor into the bed input?
- What is the open-circuit voltage on the signal line of the hotend and bed thermistor inputs?
- What is the short-circuit current of the same?
If you see differences in those last two points, that is a clue that something is messing with the divider circuit that the thermistor is a part of.
I have an MK4+MMU that I bought partially with the intent of building PLA-supported PETG and TPU parts. I haven’t dug in too far yet but in the few prints I’ve done the PLA has severely degraded interlayer adhesion. Presumably this can be addressed by purging (much) more on changes from PLA, but if I had known this before I bought, I would have seriously considered a multi-head printer.