If I understand it correctly, you only need temperature.h on the extruder controller, as it controls the temperature and sends the readings back to the mb.
I had the same problem when I updated my firmware. I believe it must have been from me forgetting to save the correct file or something. I'm sure you did, but double check that you really have the proper temperature.h, and that it uploaded correctly. Also make sure you didn't forget to comment out the other thermistor tables.
You can also try to roll back to the previous firmware and see if the problem persist. If it does, perhaps the thermistor might have loosened a bit, and now have a bad thermal connection? Try to take the thermistor off and measure how accurate it measure boiling water.
Good luck!
--
-Nudel
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