Anyone know why the temp stops 1 degree before the set value after an

@Jeff_DeMaagd OK here is the temp profile when printing with the above auto tune settings. Notice that is spends half the heat up time getting over the last few degrees.
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In the auto tune it goes right to the target and barely overshoots. In the print its like its WAY too conservative on its initial overshoot.

Autotune doesn’t do PID. It uses a form of bang-bang to determine what parameters to suggest. But you won’t get as good printing results from bang-bang

The best PID values I have are what is reported in the latest autotune.
temperature_control.hotend.p_factor 49.9
temperature_control.hotend.i_factor 1.233
temperature_control.hotend.d_factor 504
temperature_control.hotend.max_pwm 255

@Jeff_DeMaagd You were on to something. I looked at an old config and found that the auto tune values were off by an order of magnitude for P! I have to multiple P and I by 10 and D by 1.5 now its working again! Im good with a ~1 degree ripple! Thanks for the help!
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@Guy_Bailey Thanks for the suggested PID values… just upgraded to a re-arm smoothieboard and an e3d V-6 and was having similar problems.