Problem - PWM fans stop at low percentage settings

[KrzysiekX10]

Hi.
I have 5 PWM fans in my computer: 3x Noiseblocker B14-PS and 2x Noiseblocker B12-PS. They are all very important because they are on watercooling radiators, and the WC loop cools my CPU and both my graphics cards.
To get low noise, I have been controlling these fans with an automatic control in SpeedFan, according to the temperature of the primary GPU. And it always used to be like even when I set the fan speeds to 0%, the fans just spin at their minimum speeds (400RPM for B12, 300RPM for B14).
But today 4 of these fans (all apart from one B14 which is connected to the CPU fan header) started acting up and they do not spin at low percentages. Going down from 60%, the remaining B14 fans stop at 20% and the B12 fans stop at 35%. But going from 0%, they do not start spinning until I set it to 45%.
I'm not sure when exactly this happened; I was playing Overwatch and realised that my fans were strangely quiet given the graphics demands of the game. Then I looked into my case through the window and saw that 4 fans were not working. I immediately stopped the game, stopped the automatic fan control and set all the fans to 100% to cool down the components which were extremely hot by then (73 C on both GPUs), fortunately no damage occurred to CPU or GPUs.
Things I did shortly before this happened:
-Played Overwatch for the first time
-Changed my graphics cards from Crossfire disabled to Crossfire enabled in Catalyst (after setting all the fans to 100% I actually noticed that this messed up the GPU temperature readings in SpeedFan - the temperatures detected were a little higher than -1000 C (sic); but after restarting SpeedFan the readings were back to normal)
To fix this the only thing I could do was reinstall SpeedFan, but it did not help.
I would really appreciate it if somebody could say if this is a problem with the motherboard fan headers or with the fans themselves, and, in either case, what can I do to fix it?
My components:
-Fans already mentioned
-Asus Maximus VII Formula
-Intel Core i7-4790K
-2x MSI R9 290X Lightning
-Windows 10 Pro 64bit (updated from Windows 8.1 Pro 64bit)
I will give any further info if needed.

 

[FrankenDesign]

Have you upgraded to Crimson yet? Cataclysm control center could be interfering with the system somehow. I would suggest uninstalling speedfan, & your display drivers with DDU, cleaning the registry with a preferably premium registry cleaner, installing crimson (sans raptr) with the latest amd drivers then re-installing speedfan and setting things back the way you liked them. You could also prior to this clear the cmos and reset any paramters that could've strayed somehow mysteriously could just be a weird bug or something. Seems likely the software is kind of struggling over what is in charge; there seem to be a few threads competing for the sensors.

 

[KrzysiekX10]

Have you upgraded to Crimson yet? Cataclysm control center could be interfering with the system somehow. I would suggest uninstalling speedfan, & your display drivers with DDU, cleaning the registry with a preferably premium registry cleaner, installing crimson (sans raptr) with the latest amd drivers then re-installing speedfan and setting things back the way you liked them. You could also prior to this clear the cmos and reset any paramters that could've strayed somehow mysteriously could just be a weird bug or something. Seems likely the software is kind of struggling over what is in charge; there seem to be a few threads competing for the sensors.

Thank you! After doing all these things my fans again operate normally.
I would be very grateful if you could also provide some advice on how to avoid getting this problem in the future.

 

[FrankenDesign]

Make a backup of the registry with clean settings; you'll have to update such a backup regularly as you make changes to your system; otherwise upon restore all the programs you installed since then will be uninstalled. So if the settings get corrupted you can just do a system restore and it will be back to how it was. I would say make system restore points; but that is a problematic system to manage & as many registry cleaners have a backup and restore function you might as well use those.

From here on in you will have to keep hallf an eye on tracking what changes you make to the system; eventually you might be able to pinpoint the cause. Unfortunately it could be practically anything! I guess you could always submit a ticket to speedfan, microsoft, amd or anyone else you've bought stuff off. Maybe you would end up with a useful consensus of opinion? Stranger things have happened.

 

[KrzysiekX10]

Thank you very much. Actually, just a moment ago this problem occurred once again (now only the two 12cm fans got the problem), but this time the only thing I did was clear the CMOS and it already fixed it. Seems like the Q-fan control feature from the BIOS of the Asus Maximus VII Formula interferes with SpeedFan.