I would guess it is a grounding issue. I'm using the same MB and case and haven't encountered this issue. My setup is currently still on my work bench and the Morex 6577 is sitting on top of the ATX power supply I'm currently using to supply power to the MS-ATX. So it may be grounded with the power source.
As for the tight fit with the CPU fan, I got the Rosewill RCX-SC1U low profile fan from NewEgg and it seems to work out pretty well. Looks like there should be room for the stardard placement of the HDD bracket with SSD. Reviews say the fan is loud, but under normal conditions it isn't bad. It isn't until I run Prime95 for a bit that the fans starts to take off. With the case mouned under the dash, normal drive noise, and the volume of the radio - it probably won't be noticed.