I had the same problem with my mid-2012 MacBook Pro after installing Boot Camp and Windows 7.
It would boot into Windows 7 no problem, but when booting into OS X it would freeze with the beachball of death after showing the grey screen with an Apple logo. It also had no trouble booting off an external FireWire backupve.
After rebooting 5 or 6 times it would eventually load OS X, but after putting the display to sleep the beachball would return and it had to be powered off. It had no trouble booting off an external FireWire backup drive.
There were other strange behaviours too: in Windows, the keyboard backlights would come on for no apparent reason and using the keyboard backlight increase/decrease buttons had no effect.
Running Disk Utility's Verify functions revealed no problems with the drive or the partitions.
I reset the PRAM, but that made no difference.
Eventually a bit of Googling on the symptoms lead me to the support page for resetting the Intel System Management Controller:
http://support.apple.com/kb/HT3964
After following those instructions, everything is back to normal. An unexpected but pleasant side-effect is that applications now launch more quickly in OS X.
I'm assuming that something on the Windows side fiddled with the SMC and caused these problems.