I finally seem to have Metacity loading on boot, without having to manually run `metacity --replace` (and without fudging it by adding that command to the session startup list). Without Metacity, all of the windows lack title bars, scroll bars, etc, making the desktop pretty much unusable.
The things I've done recently which may be responsible for fixing this are:
1) Giving up on the NVIDIA driver (because I cannot bear the garbled startup text any longer) even though it means xgamma forgets its value on every reboot.
2) Go through gconf-editor and making sure that all mentions of windowmanager point to Metacity. Also, setting Metacity to use act as a compositing manager by ticking the box in key /apps/metacity/general/compositing_manager.
3) Deleting the saved sessions by running `rm ~/.config/gnome-session/saved-session/*` (thanks to Bernhardt at launchpad for that tip).
I suspect it was actually action 3 that resolved the issue. I'm guessing the saved sessions should have been deleted by the upgrade to 10.04, but were overlooked.
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