The issue with the fan switch, as far as I can tell, is not very common, but frankly the fact that it happens at all I find disturbing. Taking it out of play seems the simplest and most common sense option. Running the fans off of the mobo or a fan controller solves this potential issue (and gives the option of a much greater degree of control, which appeals to me).
I have a Hero VI board and currently have the rear and top/rear fan on a y-splitter connected to the fan channel #3 header, the front two fans, also on a splitter, connected to the fan channel #1 header, and the two cooler fans plugged into the CPU_Fan and CPU_Opt headers. I'm running all of them off of Fan Xpert 3 on custom profiles that provide positive case air pressure up to 85%, then negative pressure above that. When I toggle my custom Turbo mode, I have the front fans running at 85% and the CPU and rear fans at 100%. For my SLI setup, based on several months of experimentation, that gives me the best balance between cooling and dust protection during normal use, and max cooling when I'm stressing the system. (This is all with the front panel closed.) When I installed a side fan (directly opposite the GPUs) as exhaust, that dramatically reduced case temp, but the harmonics created between the fan and the grill were more than I could handle. The temp difference was 8-10C. The absolute noise level increase wasn't that bad, but it was a buzzing noise that I couldn't stand. The side fan set as intake also reduced temps but only by 2-3C. Not enough for me to keep it in place. I picked up some Akasa PWM splitters and an NZXT Sentry 2 fan controller to experiment with different control options, but haven't installed or played with either yet, so I can't say whether they're better or not.
All of the case fans that I'm currently using are Noctua PWM NF-A14s. I bought them before I learned that only the CPU fan headers are truly PWM (the CPU_Opt is slaved to the CPU_Fan header). With my current setup, I could have gotten FLX fans and gotten the same results. As it is, I have the option, via the Akasa PWM splitters, of having them all powered from the PSU, but having PWM control through the CPU header. I'm also considering running them from the GPU fan controller by adding a mini-PWM adapter - that way they'll spin up based on the GPU temp rather than the CPU temp. With my NH-D14 on the CPU, left on software profile, the CPU never heats up enough that the fans go above 50%, even when the GPU cards are screaming hot, unless I manually turn them up.
The NH-D15 has been modified to be more RAM-friendly. You'll have to check the Noctua compatibility chart to see which RAM fits, but I think most RAM can fit. I have Snipers under my D14, but you can slide the push fan up to create more room for higher RAM. I switched the stock cooler fans for the NF-A15 PWM fans - I think they look cooler, but I honestly can't tell the difference temperature-wise. If I didn't already have the D14, I would buy the D15 just to have the increased RAM compatibility, but performance is comparable.