Firefox will open a New Pop-up Window in Windows 7 Aero. When trying to Close it, it thinks it wants me to Close the Main Window. Why?

I use Windows 7 Ultimate in Aero-mode. When a new Firefox window is opened, or a Pop-up window appears, I can't close it without first clicking on that page and clicking the "X" in the corner. Instead, whenever I try to close a window that is not the first window (my main window), it will ask me if I want to close the main window with all the tabs... I have noticed some other slight quirks in this stable release as well, but this one is always present.

When I hover over the window, it does come up front, but as soon as I press the red "X" it goes immediately back to the main window and acts as if I was trying to close that one. Once in a while it will work, but shortly thereafter, it will just go back into this manner. Quite odd. This is the first time I've truly had any problems with Firefox.
In addition to that problem I have noticed a few things, but one that may be linked is sometimes I'll click a link. Although I haven't specified to open it in a new window, it will do so anyhow. This gets annoying quickly. Usually shutting down Firefox and reopening will fix this (and once in a while just leaving it be for a long time). Somehow, I think this issue is somehow linked to the one above.

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