I have the same problem. For me, it appeared when I upgraded Ubuntu to 8.10 about a week ago. I can move the window using the mouse. I can change focus using the mouse. I cannot resize the window, nor change focus using alt-TAB. If I do, the desktop freezes. After a while, it unfreezes. If desktop effects are used, there is no problem with Emacs, only when they are not used. No problem in KDE. (maybe because use desktop effects there, I don't know if I do). The ctrl-alt-F2, alt-F7 workaround works for me too.
I have the same problem. For me, it appeared when I upgraded Ubuntu to 8.10 about a week ago. I can move the window using the mouse. I can change focus using the mouse. I cannot resize the window, nor change focus using alt-TAB. If I do, the desktop freezes. After a while, it unfreezes. If desktop effects are used, there is no problem with Emacs, only when they are not used. No problem in KDE. (maybe because use desktop effects there, I don't know if I do). The ctrl-alt-F2, alt-F7 workaround works for me too.