A bunch of people have had IDE 1.6.x problems, including IDE crashes and bizarre compile errors, when they have an old 1.5.x installation. Those problems seem to be caused by out-of-date executables that the new IDE saves outside the IDE installation directory. In such cases it appears that the fix is to delete or rename the old "Arduino15" directory and re-install 1.6.x.
On Mac OS X:
/Users/username/Library/Arduino15
On Windows:
C:\Users\username\AppData\Roaming\Arduino15