After a LiveCD (2006.1 LiveDVD actually) GRP installation, installed packages that do not belong in 'system' are not added in 'world' (e.g. gnome-base, gnome-common etc). As a result, they are never going to get updated. 'emerge --depclean' tries to unmerge almost half of the installed packages (approximately 250 out of 500).
Bleh... assigned that wrong...
This is a known issue that will be fixed shortly. It's actually an issue with the x86/amd64 Live CD/DVDs, not the installer. We're currently working on getting fixed ISOs out the door.
Is there a work-around for us unlucky guys? Whatever I've read and tried (e.g. regenworld, emerge -e world) I can't get a decent 'world' file.. :( I've reached to the point where a fresh Minimal Install appears to be the only option!
Until the new ISOs are up (should be really soon), the only workaround is to edit /etc/make.conf on the LiveCD after it's booted and remove the PORTDIR_OVERLAY line before running the installer.
This is now fixed on the ISO images on the mirrors. If you want to check if the mirror has the updated ISO, look at the .DIGESTS file. The MD5 for the good iso is: f46c9bcadea4944396f6ecdd7dbf283c