After installing the 10.6.6 update and launching the new Mac App Store, a few people are noticing that the window for signing into the store seems to be missing. If Expose is activated, the window will be shown as being available, but when it is clicked the window will remain hidden.
Some have found that the main App Store window seems to be hiding the log-in window, and though it can be moved to reveal the log-in window, the window seems to be inactive and will not accept user input.
This problem appears to be associated with the presence of the FruitMenu haxie that is developed by Usanity. If you have FruitMenu installed (which allows for customization of the Apple menu and contextual menus in OS X), try uninstalling or disabling it to see if that allows the App Store to work properly.
There may be other incompatibilities such as this with other haxies and OS add-ons, so be sure to try disabling any you have if you are experiencing similar problems. If you find an incompatibility and can replicate it, we would like to know, so post it in the comments or e-mail us.