I had the exact same problem and found a working solution (for me). Original information from this blog: http://jechem.blogspot.be/2011/04/fix-plymouth-splash-screen-in-ubuntu-on.html
First install hwinfo by running the following command:
sudo apt-get install v86d hwinfo
After the installation run the following command and note down the highest resolution:
sudo hwinfo --framebuffer
For me this was Mode 0x0361: 1280x800 (+5120), 24 bits, next edit the following file:
gksu gedit /etc/default/grub
This will open the GRUB config file, we now look for GRUB_CMDLINE_LINUX_DEFAULT="quiet splash" and change it with the following, change your resolution with mine and also add the color depth (for me 24 could be 16 or 32).
GRUB_CMDLINE_LINUX_DEFAULT="quiet splash nomodeset video=uvesafb:mode_option=1280x800-24,mtrr=3,scroll=ywrap"
Then find the following line (uncomment if needed) and change your resolution again, note that you don't include the color depth:
GRUB_GFXMODE=1280x800
Save and exit, next edit the following file:
gksu gedit /etc/initramfs-tools/modules
Scroll to the end of the file and add the following line, again add your resolution and the colordepth like you did before:
uvesafb mode_option=1280x800-24 mtrr=3 scroll=ywrap
Then in the terminal type the following commands and then reboot:
echo FRAMEBUFFER=y | sudo tee /etc/initramfs-tools/conf.d/splash
sudo update-grub
sudo update-initramfs -u
For me this fixed the problem, I tried all the other suggestions and scripts, none of them worked but this does, good luck!
ls -l /var
(or put them in the question). Check for symbolic links from /run to /var/run and /run/lock to /var/run/lock. By the way: 13.04 is beta software and installing gnome-shell might be bugged. If so we can not help you. If this also happend on 12.10 I would advice tagging it 12.10 and not 13.04.