Can I schedule a periodical file permissions repair? With Automator, maybe?
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 /
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.
You can do this with a combination of iCal, AppleScript, and Shell Scripting.
First, open AppleScript Editor (/Applications/Utilities). Paste this in:
tell application "Terminal" do script "diskutil repairPermissions /" end tell
Go to File-> Save As. Select a safe but out-of-the way location. Set the File Format menu to Application.
Then, open iCal. Add a new event (call it something like "Auto-Repair Permissions"). Right-click the even and select Get Info.
Set the Repeat menu to something like Every Month (depending on how often you want to repair the permissions).
Under Attachments, click Add File... Navigate to the file you saved from AppleScript Editor.
Now, iCal will automatically (at the interval you selected under Repeat) open the app you created. That app opens Terminal and runs a command which verifies and repairs your permissions. The Terminal window has a progress meter and a list of the changes its made (along with any errors).