You mean a hiccup in the updating of the temperature display? As long as the temperature was never wrong, I wouldn't worry. When the software asks for the temperature, I think it first has to wait for the current movement queue to finish before it gets an answer, which can take several seconds, depending on the move.
If you see moderate temperature jumps it could be EMI, in which case you can try to move the termocouple wires as far away from the stepper motors as possible.
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nick-foley 5
Bet a wire is getting loose around your thermocouple board.
Or some sort of EM interference along the TC wires.
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