Cannot Update Configuration Over Existing

I am not sure if this is a bug or I am just doing the wrong procedure but whenever I want to enter a new configuration(from Knoppix/configure)I always get an error that "partition is busy or not mounted" -this pertains to the partition where I have an existing configuration files. The partition(hda5) is already mounted and read-write enabled. After the error comes out hda5 can no longer be accessed. I can access it after going as root and mounting it.

To be able to enter new settings I have to delete the existing files in that partition.

Is there a work around or am I doing the wrong procedure?I have 3.2 3-28-2003.