Still a virgin, running Knoppix from HD with a boot floppy.

I've made a few changes - fonts, mouse speed, etc. - and saved them to my boot floppy. But when I boot using Knoppix floppyconfig I get a nice message saying all of the mods are recognized and loading but none of them take effect. Huh?

What's the difference between saving these configs to floppy and "persistent home"?

I'm willing to make pretty much any changes to my Win98 HD except repartitioning (soon, be gentle).