It could be one of your Docklets isn't loading correctly. Have you tried unloading and reinstalling through Impulse?
http://www.impulsedriven.com/impulse_setup_full.exe
Go to Start > Run... (Start > Start Menu Search in Vista) and then copy this into the command line:
for XP: %userprofile%\local settings\application data\stardock
for Vista: %userprofile%\AppData\local\stardock\
It will open a file folder. Delete any ObjectDock or ObjectDock Plus folders. Be sure to save your theme before doing all of this.
Then ,when you reinstall, you should setup a few basic, built in Docklets and reboot to see if it resets the dock before you reload any saved settings.
Please let me know if you still have problems.
