[quote="mr_ed"]In general, using upgrade on Knoppix is one of those things called Not A Good Idea.

Piece A may be from "stable" and Piece B from "testing," while Piece C is custom-tailored for the job. The people assembling them know what they're doing and make sure everything works together.

But upgrade doesn't. [quote]

I agree with your first statement ("Not a Good Idea") but I have to disagree with the second. There is absolutely nothing wrong with running a mixed stable/testing/unstable system and upgrade is quite capable of handling a mixed system. What would be the sense of having applications in 'unstable' for testing if they could only be used on a 100% 'unstable' system? All upgrade does with applications is replaces the existing version with a newer version from the appropriate stable/testing/unstable repository if there is a newer version. This is no different than getting the latest version with 'apt-get -t unstable <package>'.

Where upgrade gets knoppix systems into disarray is that it also fiddles with the startup routines to try to convert everything to some arbitrary Debian standard. The most noticeable effect of this is that it sets every available service to autostart in all runlevels. Some of these (notably 'NIS') are very slow to start and there is no need to have a bunch of services you are not using auto starting. You can correct this using sys-V-init to only startup the services you want. For ones you really don't want (like Nis); 'apt-get remove --purge nis' is the way to go.

I have been told you can configure debconf (which is what apt-get upgrade uses) to not do so much fiddling or at least to ask first but I haven't tried it yet.

As you say in your second post, the start sequences are all in /etc/rc*** directories. Take a look at what this looks like on your knoppix CD, a standard knoppix system has only knoppix-autoconfig, knoppix-hd-conf & mountall.sh. Knoppix-autoconfig is not used on a Debian style hdinstall. Knoppix-hd-install shuts down then restarts internet services etc for some reason.
It has caused some problems after an upgrade by shutting these down then being unable to restart them. The cure seems to be edit the script so it doesn't do the shut down/restart.