You still have the X screen up, but you can't type or move the mouse. Continuing to command-tab will eventually bring you back.
I use xmodmap to remap command to control, in case that makes a difference.
I think this is a bug in MacOS X PB. There's no way to tell if a Cocoa app got deactivated. Hopefully they have fixed that in GM.
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This is fixed in Mac OS X 10.0. There is still some weirdness using Command-Option-Esc, which we should look into. (We should switch back to Aqua on this key combination.)
The remaining issues with this bug have been fixed in XFree86 CVS. Command-Tab doesn't do anything while showing the X11 display, but other methods of switching you to another application and Command-Option-Esc switch you back to the Aqua desktop.
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