Can I schedule a periodic file permissions repair?
Go to the terminal and execute "crontab -e" to add a new crontab entry. Now there are numberous syntaxical ways you can accomplish what you want (read about it on wikipedia). The easiest one, however, will be to put 

@monthly diskutil repairPermissions /


in it.

Note: You'll be using vi for editing. Press "i" to type, then after you've finished press ESC and type in ":wq" to save and quit.