Fan headers suddenly lost power?

I've been running into a problem with my motherboard (or possibly PSU) recently where 2 out of the top 3 headers do not seem to be supplying sufficient power to any fans. I am wondering why this would suddenly happen out of the blue..

I am running separate AIO coolers on my CPU and GPU - my CPU is being cooled by an NZXT Kraken X52, with the pump plugged into the W_Pump header, and the two fans (intake) attached to the radiator plugged into the CPU_FAN and CPU_EXT headers.
My GPU is cooled by a Corsair H55, attached by the NZXT G12 bracket. Both the fan (intake) and the pump are connected to the fan power provided with my case.

I also have one additional fan (exhaust) connected to the H_AMP header on my motherboard.

Everything was working perfectly for around 5-6 months. CPU was averaging around 28c idle, 38c load. GPU was similar - 30c idle, 40c load. This is all at around 22c ambient.

Just last week, I saw my CPU temps climbing without anything going on. At idle, it was slowly ramping up until it hit about 80c and I decided to shut down the system and investigate.

I noticed on next startup, that the two front radiator fans for the CPU stopped working. They would twitch a bit, but not spin at all. I was able to confirm through NZXT software that the pump was still running, however.

I tried swapping different fans into those headers - every fan would exhibit the same behavior. Slight movement every so often, but would not spin.

For the meantime, I've moved those two fans to my case fan connectors, though I am seeing a hit in performance from it. Maybe I'm being paranoid, but I also believe I am seeing my GPU hit higher temps since this issue. It now regularly hits 70c in games, and even higher in something like Furmark.

Is this likely an issue with my Motherboard? Or is my PSU struggling to deliver the power to my fans? Something else?

Would an internal fan controller be my best bet if I didn't want to replace any major components?

My build is:

Motherboard: MSI X99-A II
PSU: Corsair RMX 850w
CPU: i7-6800k (OC to 4.0ghz)
CPU Cooler: NZXT Kraken X52 w/ stock fans
GPU: GTX 1080ti
GPU Cooler: Corsair H55 w/ stock fan

I also typically didn't use any software to control my fans - I would let NZXT CAM control my CPU pump everything else just run on whatever stock curves were present.

Thank you for your time, and sorry for the wall of text.
Reply to bozeii
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More about fan headers suddenly lost power
  1. One sure way to burn your mobo's fan headers is connecting multiple fans to one header, using a y-cable or some other contraption, when the combined fans require more Watts or Amperes than the fan header can supply.
    But a) you haven't done that and b) judging from the way your post is written you know that and hence wouldn't do it.

    It definitely is not your PSU ... the 850W (+12V total) and 70.8A (+12V total) which your RMX850 deliver are sufficient for your build.
    In any case, it has worked before, so if something went wrong with the PSU, there'd be no power at all for the mobo ... not only a reduction of supply to random mobo components.

    The only explanation that seems reasonable is that 2 of your mobo's fan headers suddenly burnt out, somehow.
    It doesn't seem very probable, but what possible other explanation is there?

    Unless you have the necessary equipment, I guess taking it to a PC shop and asking them to measure the actual output (in W and A) of the 2 fan headers is your best bet.
    Usually a fan header supplies 9.6 to 12 Watts and 1 Ampere. Your mobo's manual will tell you what the precise numbers are.

    If those fan headers are really burnt, a fan controller would be your best bet ... get one which can be connected to the PSU by SATA, not only to the mobo's fan header, to avoid burning out your last fan header.
    And make your next motherboard an ASUS ... ;)

    Another thought:
    Are the 2 fans originally connected to the faulty headers stock fans which came with the case? If yes, I'd consider replacing them, too ... fans are where case makers save money, most pre-installed case fans suck.
    And motherboard fan headers don't just burn out like that ... maybe the fans themselves are responsible.

    Cheers,
    Gaius

    P.S.: That 'wall of text' is exactly what a good OP needs. You have described your setup and the way you connected things precisely, you said what went wrong and what you have done to test/remedy the situation.
    I wished more OPs were like that, instead of "Help fans don't work on my computer" ... and hope people can magically discern what hardware is being used and how the problem occurred. :D
    Reply to gaius_iulius
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