iTerm2 preferences keep resetting after reboot
Well. I did not find the cause for the issue (although it was quite obviously some file permissions problem). But this is how I fixed it:


Quit iterm2
Move ~/Library/Preferences/com.googlecode.iterm2.plist to the Desktop
Reboot (because plist files are protected) 
Launch iterm2 and quit it again to create a new plist file
Open ~/Library/Preferences/com.googlecode.iterm2.plist in an editor
Paste the contents of the plist file on the Desktop into the new one
Reboot