I have a multiple monitor setup and I enjoy watching shows in the full screen format. The problem is that even if I click on a different window for the sake of multi-tasking it closes the full screen window. Is there a work-around for this? Thanks.

I have that same problem and I understand how it's annoying but currently Flash does not allow any work around since the fullscreen functionality is built into Flash as is, with no configurable variables. I would suggest trying Boxee to watch our videos on the 2nd monitor since that program sort of always stays in fullscreen mode. I haven't really tried it much and don't know how well the program will run while it's not in focused view but you can read more about it here:
http://www.crunchyroll.com/forumtopic-576238/watch-anime-and-drama-on-your-tv-with-boxee/

do you know if there are any plans to add CR shows to the Windows Media Center lineup? I'm not even sure how that could be implemented without having a dedicated section like Netflix does since you'd need to take into account paid subscriptions.

and gah...doesn't seem to support 64-bit W7.

Hulu has found a nice work around for this on their flash player, http://www.hulu.com/watch/92766/dawn-of-the-dead. Go there for example and you'll notice on the side of their flash player an option called "pop out", at which point it opens a window with nothing but the flash player in it and then you can maximize the actual browser windows instead of using a flash based full screen. Right below that is the lower lights feature which is what I used before I noticed the pop out feature. I've really been hoping features like these will be put into crunchyrolls flash player for awhile, since for such a large and well organized site your flash player is relativity bad.