About 2 weeks ago the applets I had in my gnome-panel starting acting up: they would not stay in place after login/logout even if with the option “Lock To Panel” checked.
It seems that the culprit was a gconf option of applets, named “panel_right_stick”: when enabled, the position of the applet is interpreted relative to the right (or bottom for vertical panels) edge of the panel. The option can be found in gconf-editor in each applet under /apps/panel/applets.
What has happened in my system was that somehow some applets had the option checked while some others didn’t. Unchecking it for every applet made them stay correctly in place.
I hope this helps someone.