I know this post is old, but I've just found out something very useful, may help out a lot of people.
Ever noticed that when you launch Word or Excel etc from Objectdock the aero glass effect doesn't display, but if you launch the same application from the start menu it does?
The problem is not the target app's compatibility mode, it is Objectdock's compatibility mode.
So go to C:\Program Files (x86)\Stardock\ObjectDock
go to the compatability tab,
make sure the compatibility mode box is unchecked,
but ALSO click on the 'show settings for all users box' at the bottom
and make sure the box is unchecked there too. OK everything.
restart Objectdock, and launch the app, it should now be displayed in its aero glass glory.
I had the same problem with Google Chrome as the original poster, hence why I saw this post.
But currently am using Firefox 4 beta, and the aero glass wasn't showing up after launching it from OD, now it does after this fix.
I dont have Chrome on my computer any more (I love FF too much), so can't test it for that, but I'm confident that this is the solution!