I am experiencing the same behavior after upgrading to Ubuntu 11.10. Furthermore, I can see the shadow below the top panel and left panel disappear and Nautilus segfaults on startup.
** Summary changed: - Desktop icons become invisable + Desktop icons become invisible -- You received this bug notification because you are a member of Desktop Packages, which is subscribed to nautilus in Ubuntu. https://bugs.launchpad.net/bugs/841474 Title: Desktop icons become invisible Status in “nautilus” package in Ubuntu: Confirmed Bug description: after sever minutes of being logged on, the desktop items disappear, and are not click-able. re-logging in fixes the problem. Ubuntu 11.10 , version 3.1.4 of Nautilus. ProblemType: Bug DistroRelease: Ubuntu 11.10 Package: nautilus 1:3.1.4-0ubuntu5 ProcVersionSignature: Ubuntu 3.0.0-10.16-generic 3.0.4 Uname: Linux 3.0.0-10-generic x86_64 NonfreeKernelModules: fglrx Architecture: amd64 Date: Sun Sep 4 22:05:09 2011 ExecutablePath: /usr/bin/nautilus InstallationMedia: Ubuntu 10.10 "Maverick Meerkat" - Release amd64 (20101007) SourcePackage: nautilus UpgradeStatus: Upgraded to oneiric on 2011-08-26 (10 days ago) To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/nautilus/+bug/841474/+subscriptions -- Mailing list: https://launchpad.net/~desktop-packages Post to : desktop-packages@lists.launchpad.net Unsubscribe : https://launchpad.net/~desktop-packages More help : https://help.launchpad.net/ListHelp