I am running Gentoo on a Laptop and I have Linux installed on the removable HDD. On Friday afternoon everything was working perfectly in Gentoo. I had to do some work in Windows yesterday (Saturday) so I swapped the Linux HDD for the CD-ROM and did my work in Windows. Now, I put in my Linux HDD and stuff just isn't right. The boot process goes just as it has in the past, but I do not have my desktop icons, I cannot open nautilus, and I cannot make changed to the Desktop Background Settings through the GUI. I have checked my ".gnome" folder and everything is still there as it should be, but I don't have the items displayed on the desktop. I have tried to update the packages on Gentoo, re-emerge gdm, and I have run fsck on the drive, still to no avail. Any ideas would be greatly appreciated as I am still a newbe and am at a loss of what to do or check. Thanks in advance for your time and suggestions.

Nevermind, I got the issue resolved. I renamed my .gnome and .gnome2 folders, rebooted and everything went back to how it was, minus a few links that I had on the toolbar.