I had the same prob,i think it started when i tried to clear space on flash 0 (remove camera ect).
The only way i could find to get it all back was a clean flash,i also have some probs playing iso from mem stick if i mess with flash 2 much
.I keep it clean now..

I have the same prob when ever i drop in a sysconf_plugin I lose my settings area in xmb... I've tried the USB Bar mod and I can use my settings but i have the same missing parts as everyone else... does my psp just not compute with a decrypeted sysconf_plugin?