I have the same pump setup on a Maximus VI Formula. I would recommend you plug the 2 of the fans onto the CPU_FAN and the other 2 on the CPU_OPT fan headers vie fan y splitters for starters. The pump can be plugged into just about anything because it will run at a constant 2300ish RPM and cannot be controlled.
You're fan y splitters may be to blame. the may be 3 pin only and thus making you're pwm fans rather useless for fan Xpert II.... You did get PWM fans right? Although they should still be recognized by both the program and the bios.
Corsair 750D | Maximus VI Formula | 4770K @4.5 | H100i P/P | Vengeance Pro 16GB 2133
ASUS GTX 780 DCII | Intel 520 SSD 120GB x2 | EVGA Platinum 1000W | Windows 8.1