I just noticed your signature @Entz indicating your membership in the ZESS. That's funnyIf your running a fixed RPM why not use the speed dial to set it to that speed and not use your motherboard (other than for speed monitoring). Perhaps there is a ramp or something on the PWM side and the pump cant start.
Just to confirm you are still powering it with molex right? There are not designed to pull power from the motherboard.