System is Mountain Lion, these steps will reproduce the problem:
Select a primary resolution in System Preferences pannel, Displays. Select the 'Best for Retina display' (Other resolution in this pannel is also OK).
Use the SetResX to set the resolution to 2880x1800 (I tried some other programs, the same result).
Restart the system or log out the current account.
Then after login again, the resolution will restore to the resolution in setp one.
Is there a way to keep the resolution to 2880x1800 permanently?