The only thing that I can this of is make sure you turn auto off, and then hit apply. The fans won't change unless you hit apply.

get driver sweeper from guru3d. Once it is installed, remove the NVidia bits from program/feature in the control panel. Then use msconfig to boot in safe mode. reboot. Once in safe mode, run driver sweeper and remove all trace of NVidia. Run msconfig again to boot normally. reboot.
After that install the latest NVidia drivers. That always fixes weird stuff like this for me.

Go back to 331.65, after driver cleaner, fixed for me.

Sometimes a program like asus suite that has overclocking enabled will do that. Might want to start looking at profiles that could be taking over after boot.
 

Ok after a LOT of testing i finally figured out what the problem is.
 
Apparently the GPU Boost 2.0 (or the nVidia drivers) checks the fanspeed of your gfx card. If the fanspeed is below around 1300 rpm then the software will override the fanspeed and not allow it to go any lower. My guess is that it's is some sort safety feature coded into the software. Hopefully they can change this as it makes no sense to have this check as long as the temperature of the card is low.
 
This problem will apply mostly to people with "silent" aftermarket coolers that have large 120/140 mm fans with speeds of sub 1100 rpm.
 
If you want to check this problem out yourself and have a card with dual fan cooling, try to stop the fan that outputs the rpm with your finger and you would notice that the remaning fans speed up to 100%.
 
[edit] when this override happens Precision X will still say and log that the fan speed is at lets say 41% (manual or auto does not matter) even though the fan is at 100%

digitalbath88 can you use HWMonitor to check the rpm of the fans (both cards) ?

I recently just bought the gtx 770 SC with ACX cooling also, and I have the same problem where my fans would reach 100% after I reach the windows login page. Does anyone know how to fix this?
 

Give this a shot guys...
 
Here is how to force your cards fan speeds to 30% & 100% as needed.
 
#1 Download NVIDIA Inspector & WinRAR to desktop. Install WinRAR First.
- http://download.orbmu2k.de/download.php?id=51 
- http://www.rarlab.com/rar/winrar-x64-420.exe 
 
#2 Install NVIDIA Inspector. 
- Right click on NvidiaInspector.zip on the desktop and select "Extract files...", Extract to Destination Path "C:\Program Files (x86)\nvidiaInspector" without quotes. 
- Press OK to start the extraction. 
 
#3 Create 30% Fan Speed & 100% Fan Speed .bat files for Nvidia Inspector. (These two .bat files will allow you to force your fans to 30% & 100% as needed.) 
- Open 2x Notepad (Click Start and type in Notepad and hit Enter.) <<Do this twice. 
- Copy and Paste this... "C:\Program Files (x86)\nvidiainspector\nvidiaInspector.exe" -setFanSpeed:0,30 into your first Notepad, Save AS... 30% Fan Speed.bat and save to Desktop. 
- Copy and Paste this... "C:\Program Files (x86)\nvidiainspector\nvidiaInspector.exe" -setFanSpeed:0,100 into your second Notepad, Save AS... 100% Fan Speed.bat and save to Desktop.
 
Once you have created the above .bat files just double click on them and watch your cards change fan speeds. Hopefully it works out for ya.
 
 

hey Whuang02, thanks for in information.  I just brought mine a week ago back and experience the same problems posted here.  I checked the fans, and sure enough one of the cables got loose and stop one of the fans from spinning.   After I reseated the cable, the fan noise is back to normal.  Thanks again. :D   (wasted so much time thinking it was a software problem.. all I had to do was open the front panel and shine a flash light).
 
 

Many thanks to whuang02. Unfortunately, mine appears to be a dead fan, but at least now I know what the culprit was.

whuang02 youre the man! I was messing with this issue all day and never thought to check if one of the fans was snagged. Turns out one of the PCIe power cables went up into one fan and stopped it. Removed the cable and all is well.
 
Thanks!