Ok, figured it out, I am guessing something got messed up after one of the upgrades. Was running 4.0 until about 3 weeks ago, upgraded to 4.5 back then. Upgraded to 4.6 yesterday. Profiles must have gotten messed up during all of this. I changed profile setting to 99mm and resaved the profile, than changed it back to 4mm and saved again and it started working. Now the value changes when I switch profile or material.
This depends on what is set in the quality profiles for your printer. Anything defined in a quality profile or in the custom settings panel overrides what is set in the Materials preferences.
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