This is happening on hardware that either has less RAM or slow CPU, or both. I got this problem on my Ntavo thinstation (400MHz, 256MB) and the Classmate (900MHz, 256MB). The first time I booted Jaunty pup on the Classmate, I got the desktop ok, but not on the reboot. After that, it has been ok.
I don't recall the exact message, but in /tmp/xerrs.log ROX-Filer reports something is not responding and terminates. It is Rox that manages the desktop icons and background.
ROX-Filer is started in /root/.xinitrc. I have added some extra code that checks to see if ROX-Filer has quit (just before launching jwm) and if so attempts to restart it. I don't know if this works, as the Classmate now refuses to exhibit the problem despite many reboots.
I also put a check into /sbin/pup_event_frontend_d, so that it won't start sending pinboard modification requests too soon.
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