Have you tried creating a new account and see how your Dock works in that User acct? (That will tell if your problem is systemwide or limited to your User acct.)
Open System Preferences > Accounts > "+" make it an admin account.
If this works, then log back into your problem account and navigate to ~(yourHome)/Library/Preferences and trash this file:
com.apple.dock.plist
Then log out and back in again. Or restart.
(You will have to reset a few finder prefs the way you like them.)
Let us know.
-mj
macjack@gmail.com