Random Fans Not Working Unless Sleep/Wake

[Daharen]

So I have mostly gotten this all worked out, as it stands now, I have to start the computer, and once its started, I put it to sleep, and wake it up again, and now all my fans work... However, this is ridiculous. Before I did this I had issues with some fans not running at all, inconsistent speeds on other fans, random starts and stops, and countless other things. I'm using  Noctua A12x25 fans, there is no correlation between which fans stop (Some are directly connected, some are through hubs, some are using splitters, and different motherboard connectors are acting up at different times). 

I am 99% certain this is some sort of software problem. What makes me say that? When I load to BIOS all my fans start, and remain at 100% no problem, it only goes whacky once I am into the OS. I can't figure out what is going on though. I've tried all sorts of different software, including installing and uninstalling them and trying them each individually, and I'm at a loss. I've used SpeedFan, Argus, and EasyTune specifically. Initially  with them all installed, and tried one at a time by disabling the others, and restarting with only one enabled. Then by uninstalling all of them, and installing only one at a time, and restarting between each cycle. The problem persists. 

I can only thing some setting in my motherboard that is only loaded after the BIOS kicks in is effecting power delivery to the fans, but I can't even imagine what that would be, or where I would start, as I have looked for options  like that to change to fix the problem and found nothing. I'm at a loss, and while the problem isn't a huge deal since I can just put my PC to sleep and wake it up and fix the problem, it is more than a mild annoyance. 

Also as a follow up, I have disconnected all the fans, and reconnected them all to the motherboard, and the hubs. I have also removed the CPU, and reinstalled it in case it was some bad pin connection or something. Neither of these had any effect. 

[For Science!]

Try a linux distro to rule out hardware issues. I suspect some program left some registry entries or the like in your windows and so you might have to clean install.

[Daharen]

10 hours ago, For Science! said:

Try a linux distro to rule out hardware issues. I suspect some program left some registry entries or the like in your windows and so you might have to clean install.

Alright, I'll have to wait a week or so, but sounds like a reasonable solution. Hoping your wrong of course since I have some software with limited use downloads that I can't reinstall if I do have to do a clean reinstall, but if that is the case, I guess I'll just need to suck it up, I'll report back in a bit.