Update - I decided on using AI Suite 3's Fan Xpert again. Figured I would calibrate the fans in BIOS and use Fan Xpert in Windows 10 for fine tuning while under that environment.
Are you saying one overrides the other? Maybe I should reset the BIOS to default to clear the Qfan settings, re-overclock and stop messing with it. As long as the AI Suite takes over every time I boot into Windows I'm fine with that. Plus sometimes Qfan locks up when playing with the fan curves in BIOS.
In the UEFI BIOS the Qfan calibration wants to set my Thermalright Silver Arrow ITX heatsink cooler fan at 99%-100%. In Windows the Fan Xpert calibrates it differently with a more normal range of operation. The 4-pin PWM fan is plugged into the correct CPU Fan header. So I just have my fans set to the Turbo profile in BIOS. I'm trying to use custom curve fan profiles in Windows. Still Experimenting with that vs Turbo which doesn't seem that loud with my Phanteks 140mm case fans and the 140mm Thermalright "ROG" style fan they use.
(New version of AI Suite 3 is out and new CPU-Z Pro Gaming version now shows the correct Vcore value BTW.)