Mine used to do that, I did the same as you, stuck some padding in and I reduced the read speed of the drive because I noticed that it would make alot of noise and shake quite a bit too. The padding and the lowering of speed (12 down to 8) helped but it would still scratch discs but less frequently.
Last week I had to replace the laser as it was having problems reading, dirty disc errors, since the laser change I've noticed that it's alot quieter and doesn't shake so much and I'm hoping I don't get anymore scratched discs.
BUT
I've got my Sammy replacement drive today because the combo of laser death and a history of scratched discs kinda pissed me off so once I put that in I won't know for certain whether or not it was scratching due to a weak laser but I'd suggest a laser clean / pot adjust / change and see if that helps. My scratching drive is a hitachi 47dj.
I got my sammy today, made my usb stick with iprep, whacked in my via 6421 pci card in my desktop and I've just realised that my desktop is too old to boot from usb, I'm going to try the dreaded floppy route. As I already have my key and all I'm doing is spoofing I'm hoping my risks are minimal.