Do you have any other monitoring software installed and running? EVGA Precision? NVIDIA System Tools? HwMonitor? Speed Fan? Etc...

Having more that one piece of monitoring software installed and running can cause these sorts of problems.

I'm using the 260.89 WHQL (not beta) , MSI afterburner 2.0.0. & Win7 x64 too the only difference is I have a 480 1480-AR.
I have not had any issues like that at all.
I use the AB profiles once you have it set the way you want it hover your mouse over the number where you want to store it (next to "Profile" bottom Left) then right click your mouse and the current setting will be saved to that number. However you are not done yet if you want it to start with windows. You will need to 1st click Apply then make sure the green light is on next to "Apply at system startup" Now that should do it the next time you start windows it should be where you left it.
You could also check AB settings, just click on the Settings button bottom right,  and make sure on the general tab 'start with windows' , is checked and on the 'Fan" tab make sure the 'Enable user defined software automatic fan control" is unchecked. I know that doesn't sound right but it works for me and is the default setting.
If none of the above works then I suggest you reinstall AB make sure to trash the original download and download a new package.
If that doesn't help you may want to reinstall the GPU driver same way download a new package
Good Luck!