If you don't put any fan setpoints in the custom profile, it should NOT be adding automatic fan commands based on slowdown of a layer!!
The logic of fan speed settings are as following:
1. If the layer is not included in the Fan Control List, it will use the default fan speed.
2. When the real print time of the layer is lower than Minimal Layer Time, the print speed will be reduced and the fan speed will be increased.
3. Seems the layers you met problem with are all being reduced in printing speed, as the default inner shell should be printed with 40mm/s, but in your gcode files they are all lower than 40mm/s.
4. The fan speed will be between the speed value in Control List and Maximum Fan Speed. If the layer is not included in Control List, its fan speed will be between Default Fan Speed and Maximum Fan Speed.
5. If the Layer Print Time is too low which need to reduce Print Speed a lot, the Fan Speed will directly use the Maximum Fan Speed.
If you want to make this a proper feature, fine, call it automatic fan control and put a checkbox in the profile, explain it's function is documentation, and list it as a feature in proper release notes.
But don't backdoor the entire user base by adding a hidden feature and functionality that puts a bunch of gcode commands in gcode and NOT tell the user until they complain that this is a seriously broken system.
And what is again, completely just insane about this is, at what point was somebody going to explain this feature to users in documentation!!!!
Only after the poop hits the proverbial fan???
I still like your printer and your hardware, but I'm trying to figure out on what planet you guys are on as far as software release, version control, proper testing, proper documentation.