I'm using TM with the Missing Drawer plugin and this fullscreen plugin. When I click the first TM window into fullscreen, it works great. But if I open a second file or directory, it opens in its own fullscreen window, but leaves a gap at the top, the same height as the menubar.
Are you running 10.7 or 10.7.1? This issue appears to have resolved itself in 10.7.1.
I'm on OS X 10.7.1.