Not sure about your reasons/resolves on the saving configs on the drive, I think, even if you are user "knoppix" the save functions use root to write and read, so permissions shouldn't be the issue... hmmmmmmm...

I think the reason why you can't delete the files in Knoppix, is permissions though - the user knoppix is not root, and permissions for those files, I think, are root owner and root group, with read access only for group Other - which is what the user knoppix is - other.

What I would try...

Run a shell console, do a su, mount the hda1 device, go to the mount point for the device, locate the knoppix and configs files, and do a rm of them, as root. If that fails, I'm clueless.

When I first started out, I did the knoppix and configs, and after a few weeks, started doing the persistant home thing - I never had problems with any of these three things having write, or read, problems - I did find out that if you let Windows (any version) run defrag on the drive, my persistant home, and swap, (files) got all messed up, and Knoppix would report during booting, they were corrupt - so heed that warning. But, never, other than defrag problems, had problems using the save config, save knoppix, persistant home, or persistant swap setup. ( I did all of these with Knoppix v3.2 -=- I then hard drive installed v3.3 - so I am not sure of those "save" features in that version )

Hope this helps, Eradicator,
Cuddles