When I create a gnome-panel and I delete it, it reappears at the next login on Gnome. I use Gnome 2.0.2 (with all latest stable packages). I fill a bug at gnome.org and the maintainer said that it could related to the Gentoo Gnome package.
Do you logout correctly ? Does your .gnomerc-errors show anything ?
I have this error a lot of time (gnome-panel:4141): Gtk-CRITICAL **: file gtkwidget.c: line 2933 (gtk_widget_event): assertion `WIDGET_REALIZED_FOR_EVENT (widget, event)' failed
I close this bug. I found that the panel shouldn't be compiled for -03 as I did, because sometime, bugs appear.