Hi there.
I'm working on Fusion Unity bugs right now. I'd like to make sure I'm understanding the two issues you are seeing:
1) right-clicking a program in the Windows task bar
Does this only happen when you have the taskbar at the top? If you exit Unity, move the taskbar to the bottom of the screen, and then enter Unity again, do you still see this problem?
2) running 2 IE windows, click on 2nd one and focus instead goes to the first one
How are you clicking on the IE windows here? Are you using the Windows taskbar hover preview window to select the window you want and then the other window gets focused instead?
Thanks very much for reporting the bugs! =:)