Hmm, so have you found which fan is the noisy one yet? I'm putting my money on the Window one!
The cables look good in the top pic very neat
and as Pob said the reason for flipping the PSU would have been to get the fixed cables closer to the motherboard, as you have managed to make them reach now that is a mute point
If the run the fans in free air (on a table or in your hand, watch out for the blades!) do they make much noise? Also try connecting the same fan to the motherboard and then power it from a molex and compare the airflow (subjectively) if the airflow seams significatly different then the motherboard headers are controlling the fan speed and 1200rpm is not the maximum they will spin at (I would expect 1200rom fans to be almost silent, not quite but almost).