maybe you're running that gdm abomination which has 'Run Xclient script' as the default
This cannot influence the start of the programs I believe, unless the start of some programs are inserted in the file ~/.xsession.
So peterhodges, you can check the content of your .xsession file and paste it here, and you could follow shedyed suggest and select the configure option at login screen, type in your root password, and check what session is selected. If it is Xclient script, then switch to E17.
Also try starting out with a brand new profile in Settings>settings panel; the minimalist for example
shedyed, this is not an abomination, just another way to setup things. This method needs to be precise in the configuration of the .xsession file though (in other distros it is the .xinitrc which is used, but this version of GDM just ignores it... )
Regards,
Mélodie