When modifying startup facilities with ntsysv, linuxconf in unaware of the
changes and still has the old startup settings. This becomes problematic if
both programs are used.
ntsysv tries to modify only the current runlevel; linuxconf follows
older ntsysv behaviour and modifies all runlevels. This isn't
precisely a bug in either, just a difference in behaviour. You can
see what is going on with chkconfig --list.