Haven't figured those out myself yet, but is happening to me also. Been
working on a MySQL problem that think might have worked out. So might
be tackling this soon myself. But they are a problem.

Also, if you update-rc.d start/stop scripts in /etc/init.d like cupsys and
use the 'cleanup' option in the remaster scripts, they will delete those
from /etc/rc*.d so they won't be there either. I commented out the
only place found them in the remaster scripts and still does it.

Added to my KDE menu and changed the background and they all
get reset, all get now is the original menu and the background from
bootup (that I did change so isn't the default). Seems like it really
wants to use the persistant home feature. Hmmm, which makes me
think: Maybe do a persistant home, save that "somewhere" and see
if that works. I say "somewhere" cause want to try and make it on
the CD, but not sure where to put where the scripts wouldn't delete it.
Or might not include it in the compressed fs.

One thing I have done, little time consuming, but run the 'cleanup', stop
it before starts to compress and start over without the 'cleanup'. I am
saying this for the persistant home on CD or your NOTES, or startup
scripts added, cause the background and menu will still be back to orig.