Taco.22,
The problem is
not consolekit. The version number for consolekit, libck-connector0 and libpam-ck-connector is still 0.4.5-3.1. That hasn't changed since July 30th, 2012, as far as I can tell.
darrel@Village:~$ ls -l /etc/X11/Xsession.d/90consolekit
-rw-r--r-- 1 root root 1027 Feb 29 2012 /etc/X11/Xsession.d/90consolekit
darrel@Village:~$ ls -l /usr/share/pam-configs/consolekit
-rw-r--r-- 1 root root 169 Jul 30 2012 /usr/share/pam-configs/consolekit
darrel@Village:~$ ls -l /usr/share/polkit-1/actions/org.freedesktop.consolekit.policy
-rw-r--r-- 1 root root 1652 Jul 30 2012 /usr/share/polkit-1/actions/org.freedesktop.consolekit.policy
darrel@Village:~$
The remastersys file is correct, too.
darrel@Village:~$ ls -l /home/remastersys/remastersys/dummysys/etc/X11/Xsession.d/90consolekit
-rw-r--r-- 1 root root 1027 Feb 29 2012 /home/remastersys/remastersys/dummysys/etc/X11/Xsession.d/90consolekit
darrel@Village:~$
There's something else going on I haven't narrowed down. I just burned the DebWeb_RC3 iso to a USB drive and booted from it. It has the same Thunar version 1.2.3, which allows me to browse the hard drive with no permission errors. I started xterm, and it has the black background. Then I shutdown the machine with no permission errors.
Maybe you can figure something out by comparing the DebWeb iso to yours. I haven't started doing that yet. Nor have I tried the DebWeb_1.0 iso, because it uses the latest version of Thunar. (I have to replace wicd with network-manager-gnome on that one, anyway.) As soon as the iso has uploaded to my Dropbox account, I'll post the link.
EDIT: Here's the link:
https://dl.dropboxusercontent.com/u/31006290/DebWeb_RC3.isoIf you'd like to free up some space before remastering, all of the Plymouth themes are installed, but none are in use.