I've a pretty complex set of profile scripts that are execute when the interactive shell is first execute. The profile scripts are broken into sub-scripts and are loaded using source (".", actually).
When I "su - <user>" to my user, the scripts load as expected. However, when I log in to my shell from my Gnome session (initiated by gdm), two things seem to be different: the aliases which I've defined in a file that I source from ~/.profile aren't being loaded, and second, the value of PS1 isn't updating to what I've set in .profile (in fact, I can't seem to trace where PS1 is being set).