I've found mentions of this problem in Lucid Lynx, but this is a recent development for my system, since I've been running Ubuntu since Gutsy Gibbon.
On start up my gdm theme/icons appear for a second, but by the time I've entered my keyring password the theme reverts to the system default (what Synaptic package manager looks like). It also does not load my start up programs Gnome-Do and Screenlets. My theme only appears if I go into the Appearances menu, and Gnome-Do only starts if I pick it from the Accessories menu (and I've gone into Gnome-Do's preferences and clicked on "start GNOME-DO at login"). About once in a blue moon it will load everything correctly.
running Toshiba Satellite A-135, Intel, nvidia, about 4 years old.