Indeed, I've had a Creative CDRom that would refuse to read properly some disks, but just from time to time!
I think I have that same CDROM drive, old Creative 12X beast or some such, plays audio fine (has built in controls in front of it) but sketchy butt CD reading, I usually just get read/wrtie erros with mine (at which point I tell CacheCDFS to try again)....
Also: 3.9 should be able to be read by the primitive CD file system on the 3.1 disks.
An 80000004/3 is usually casued by some program/command in your startup-sequence effing up, hold down both mouse buttons, tell it to boot with no S-sequence and see if that helps in the short run, if it does, than go thru the sequence and get rid of all the uneccesary bits (just put an ; symbol in front of the line so you can restore it later)
ED: this isn't too unlikely, as OS3.9 added in some bits that I think some software hates, I have been warned with the accelerator I recently bought for my 2000 to disable the rom patches in OS 3.9.2 ... (I use 3.1 atm)