Did not have the same problem but solution to the 'issue' I had in using fan controller or motherboard to control rad fans might be of use.
I built my first watercooled rig not long ago. Triple radiator being cooled by 3 Akasa Apache fans (+ 3 further fans comprising 2 x 140 intake at bottom of case - 800D - and (until recently replaced with a further 140 ) a 120 Piranha intake at the top/back of the case.)
Using an Akasa pwm fan splitter as not enough connections on the lamptron fan controler (only 4)
To begin with set it up so that the 3 Apache fans were controlled via one connection on the lamptron with the remaining 3 connections being occupied by the other 3 fans - could not get it to work in the way I had hoped (my fault not the box!) so decided to get rid of the splitter and run the 3 rad fans on seperate connections ; rpm of each being manually set (with a little varience of course) at the level of quiet!
however this left me with only the one connection to the lamptron which I used by using a splitter to connect the 2 140 fans to it, BUT this left no spot for the rear 120 Piranha fan.

Placed the piranha fan in the motherboard cpu fan slot(pwm controlled - silent setting) ; no problem
except when playing Bioshock I noted that the piranha fan was being ramped up- presumambly because of the heat the cpu was producing and which was not being shiffted fast enough.
Decided that I like the idea of the cpu cooling fans going faster if need be and do not like the idea of reminding myself that I should up the speed so....
Reverted to using the motherboard pwm cpu slot - the 3 rad fans on the splitter and then such plugged in to the slot.
Works like a charm - silent most of the time but will ramp up when needed and all fans at same speed
The fan controller now controls the 3 x 140 intake fans on 3 seperate controllers (leaving one currently spare) - which do not need to be adjusted.
My thanks , again, to the person who converted me to using Pwm for cpu cooling a few years back
