There is no extension for the floppy drive. Its driver is built-into the ROM of the Mac, and may also be inside the system file somewhere. The CD-ROM has an extension. Neither likely have prefs files either though.

It's possible that the system file was screwed up in such a way that it acted goofy with floppies. It could also have been the Finder, but we'll never know for sure. There could still also be a hardware issue that shows up only in Mac OS 9, so there are a lot of different places this problem could have been.