As I read your post, and how you are enjoying the multi-monitor support of Windows8, I get the impression that you are using your 3 monitors in an 'extended-desktop' configuration. Can you confirm that?
Creating an Eyefinity Group makes the OS think you have just 1 monitor in use, and so an application expanding to full-screen across the 3 physical monitors would be the correct behaviour.
You may find luck in third party applications like Ultramon, perhaps.
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