@ sveetsnelda
Nothing happens, it just stays at auto.
Sorry to have to get so specific. I am trying to narrow it down. If I understand you correctly, you make a change in cgminer and the fan speed still *shows* auto, or the fan speed shows the value you entered but *acts* like it's being auto controlled?
One of the fans that I replaced ended up behaving in a similar way. I replaced 2 fans, put in the cards, changed the fan speeds, and the fans both reacted to the change... but one of the cards went back to auto control in a second or two. It didn't actually say that it was auto, but the card's controller took over and disregarded my setting. The RPM sensor was perfectly accurate. Sometimes it would bounce between auto control and the setting I applied. It was odd.
I removed the card and looked at the connector with a flashlight. The seat for the connector had slid up the pins a bit and I carefully pushed it flush with the PCB with some needle-nose pliers. It's been fine ever since.
You can run these fans at 100 percent if you keep them very cool. If you let the spindle of that fan get very warm though, the bastards self-destruct. Spinning them at 100 percent generates a lot of friction/heat in there. The fan by itself is fine at 100%, but if the card adds enough heat to hit a certain threshold, part of the assembly melts and the fan starts to wobble. The wobble turns into a grind and you get this really cool grey dust all over the place from the magnets sanding each other down.