A Quick Question About Icons

Hey guys, I just picked up Objectdock, and I'm still working out the kinks, but I had a quick question that I hoped could be answered here. My problem is that both iTunes and Chrome seem to be messed up.

I took a screencap of it  so you guys could see. I currently have a few programs running, but the Chrome and iTunes icons reappear on the far right, seperate from the original icons on the left. It's mainly irritating because when I click on the left icons (to bring back a minimized window) it tries to start a new window of the program, even though it's already running.

All I want is to be able to click on the leftmost icons for minimizing, but the dock can't seem to link them, or recognize that they are in fact currently running.