Reset PRAM the same as Macs always do, opt-apple-P-R keys at boot, let the computer resest a few times, (Apple recomends 5 times for some conditions, a couple should usually be OK), but sounds like you're talking about rebuilding desktop file, hold the opt-apple keys when classic starts to load, if you have separate partitions or drives, all will rebuild, OS X volumes don't seem to do much. Problem with CD, does trash empty when CD is ejected? then might be a permanent problem on CD, Could be a preference file somewhere??

someone who knows more about the Inner FIles in OS X should be able to give some hints about this?!?!?