All the fans are 24V fans, but geeetech forgot to set the jumper JP2 on the board near the fan connectors. Without the jumper all fans get only 12V. Full 12V lets the part cooling fan just spin, but pulse modulated with less than 100% is too less to let it run.
Just set the jumper and you should be able to get much better control. If you don't believe check the schematics for the board on github as I did.