The run dialog restores its geometry differently depending on whether "advanced options" were displayed last time; opening the dialog after closing it with full options displayed shows only two items unless the window is resized (or advanced options are turned off.)
Probably needs an if(advanced) set_larger_default_size() chunk of code in there.
We (Red Hat) should really try to fix this before next release.
Should be fixed with gnome-core 1.4.0.4-16