Similar problem here. After installing mountain lion, it ran fine for about 2 weeks, then while working out of nowhere my screen went a little brighter, than to the grey booting screen, and then back to Mac OSX. All the apps closed and reopened slowly. At first I had no idea what was happening but since I only have one user I guess this is a logout but with immediate login afterwards.
This happend roughly 20 times in 7 hours. In the crash logs, the crashing application alternated between WindowServer and Adobe-Software, depending what I was using at the time.
Once I read this thread and disabled multiple desktops in mission control, didn't touch it since, the problme's gone for now.
I installed the third party program TotalSpaces after installing Mountain Lion, after noticing out what functions where gone from Mission Control (I hate Mission Control with multiple monitors!), that where in the original spaces in 10.6. I disabled the app after expiencing the first few crashes, but that didn't fix the problem. However, since the app alters the Dock, it might be related.
Specs:
Mac Pro
Early 2008
Processor 2 x 2.8 GHz Quad-Core Intel Xeon
Memory 12 GB 800 MHz DDR2 FB-DIMM
Graphics ATI Radeon HD 2600 XT 256 MB
Software OS X 10.8.1 (12B19)
I got two graphics cards installed and four monitors plugged in.