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.