I Have a message in my dock that says, "Your network settings have been changed by another application" I have no idea how this happened. Now I cannot restart or shutdown my computer. Can anybody help? Thanks

This appears to be a problem related to the latest security update to 10.4.x - several threads out there suggest the following process to fix:

"Go to Library/Preferences/SystemConfiguration and delete the following (suggest make copies to the desktop first if in doubt):

com.apple.airport.preferences.plist
NetworkInterfaces.plist
preferences.plist
com.apple.nat.plist

All these files will regenerate as necessary when the associated system features are accessed. If you're using Airport or Internet Sharing you'll have to reestablish the appropriate settings, because these will have been lost when the preferences files are removed. Small price to pay, however for a permanent, and very simple solution to this irritating problem."

The .plist files are preference files, which is where your application preferences are stored. Since there are a lot of complaints out there about this one, I assume Apple will be providing a fix reasonably soon.