I see similar behavior with Pidgin. The first reboot after installing Pidgin seems to fix this.
I also have the problem that ghost emacs icons appear in the alt-tab window switcher, meaning there are emacs icons there that don't correspond to any emacs window and switching to them doesn't do anything.
GNU Emacs 23.3.1
3.0.0-14-generic #23-Ubuntu SMP Mon Nov 21 20:28:43 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux
I see similar behavior with Pidgin. The first reboot after installing Pidgin seems to fix this.
I also have the problem that ghost emacs icons appear in the alt-tab window switcher, meaning there are emacs icons there that don't correspond to any emacs window and switching to them doesn't do anything.
GNU Emacs 23.3.1
3.0.0-14-generic #23-Ubuntu SMP Mon Nov 21 20:28:43 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux