Deleting the preference file for the dock may help. I'm not exactly sure what the program modified. The preference file is located at ~/Library/Preferences/com.apple.dock.plist The ~ means your home directory. Before deleting the file just move it to the desktop (or somewhere). Now open Activity Monitor (Applications/Utilities/). Look through the list for Dock. Select it and choose Quit Process button at the top left. The dock will restart itself.
If that fixes things, then just delete the file, otherwise you can restore it back. A new file will likely have been written back (because the preference files recreate themselves), but you can overwrite it. Then just quick dock like before so it resets.