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Rampage VI Extreme Omega Fans, etc

Level 11
The board is a Rampage VI Extreme Omega. On cold start the fans blast at high speed, but then on restart they then function normally. But this is every time.

Here is a little history: The thing was crashing a couple weeks ago (despite reinstalling Windows and being fine for a few weeks) so I reinstalled Windows (a second time in a couple months)--which stopped the crashing (temporarily). After that I installed AI Suite III but Fan Expert would not control the fans as set up unless restarting (same as above) so I again installed Windows, removing AI Suite III. But that has not fixed the problem.

Edit: I don't know what I'm doing wrong with this thing, to be honest. It worked like a charm for almost a year. Then it started crashing, and then it would not play well with the latest Bios, with the clock speeds on the CPU running insanely fast and hot at default (no overclocking) so that the second newest Bios had to be reinstalled. Now it crashes regularly (it had stopped crashing until today with the latest Windows reinstall) and now the fans are not controllable without restarting the thing.

Level 8
I'm guessing that you are talking about the 2 small fans in the heatsink over the VRM. I have Rampage VI Encore and it has the same setup.
When I used Fan Expert in AI Suite it prompted me to run the fan tuner and after I ran it the two small fans screamed like two angry hornets (very loud).
I tried to slow the fans down with fan expert but it wouldn't let me slow them down but you go into the BIOS to the Monitor tab and adjust the duty cycle of those fans , then you can slow them down in Fan Expert.
The easiest way is to uninstall AI Suite as you did but it still leaves behind a fan profile unless you use the AI Suite Uninstaller as in the link:
In my case I reinstalled AI Suite without running the fan tuner and now they run at 5K RPM and don't make intolerable noise.
Hope that helps.