I have similar problem. I see lots of Nautilus windows in wnck-applet,
but when I tried go to console (Ctrl+Alt+F1) and kill 'em all, I didn't
see any processes. After returning to the Xorg, all "fake" windows were
removed.

user@user-G31M-S2L:~$ lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 11.04
Release:        11.04
Codename:       natty

user@user-G31M-S2L:~$ uname -a
Linux user-G31M-S2L 2.6.38-9-generic #43-Ubuntu SMP Thu Apr 28 15:25:15 UTC 
2011 i686 i686 i386 GNU/Linux

user@user-G31M-S2L:~$ dpkg -l "gnome-panel"
ii  gnome-panel              1:2.32.1-0ubuntu6.5      launcher and docking 
facility for GNOME

user@user-G31M-S2L:~$ dpkg -l "*wnck"
ii  python-wnck              2.32.0-0ubuntu2          Python bindings for the 
WNCK library

/var/log/syslog contains lots of messages about nautilus segfaults, so I
think that it might be useful and I attached it here.

** Attachment added: "syslog"
   
https://bugs.launchpad.net/ubuntu/+source/gnome-panel/+bug/701469/+attachment/2151798/+files/syslog

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https://bugs.launchpad.net/bugs/701469

Title:
  wnck-applet generate a infinite windows

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