I’m pretty sure I’ve had this happen but only very seldom (Mac OS 10.6.8) and noted nothing noticably recreateable about it; for the cases when I have to trash prefs I have set up a Script that resets many settings to what I want them to be – not all tools’ settings in the Options Bar are easily set thusly though unfortunately.
Not once for me, I'm happy to say.
You can copy the entire tree of files you find at the following location to effect a preferences restoral.
C:\Users\YourUsername\AppData\Roaming\Adobe\Adobe Photoshop CS6\Adobe Photoshop CS6 Settings
Scout around in that folder structure, you may be able to discern subsets of files you want to restore individually.
Also, if you do regular Windows backups, you may be able to use the Previous Versions feature to get back the last backed-up copy of particular files, for example:
C:\Users\YourUsername\AppData\Roaming\Adobe\Adobe Photoshop CS6\Adobe Photoshop CS6 Settings\Adobe Photoshop X64 CS6 Prefs.psp
I have never experienced this resetting of Prefs, going back to the first PC version of the program.
Something is definitely up. Have you had any wonky I/O behavior, such as file corruption on a HDD?
Matter of fact, I have had to reset my Prefs only once in almost 20 years, and that was when Set Point (Logitec) driver decided to update, while I was Saving a large HDR pano. [Thought that ALL updaters were OFF, but I had missed one - never again!]
I'd run a CheckDisk on all of my drives, and especially on C:\.