For anyone watching this bug, i believe it is closed by the enhanced diff mode (merged in salsa (thanks Marcos!), and pending an upload):
Once the version in salsa is uploaded if If you add DIFF_MODE="true" to /etc/chkrootkit.conf then the cron job will filter the output to give you stable output when common network managing tools are employed (there are instructions in the output as to how to then mark the output as 'expected', and then you will get no output. ) (I still think there is more that could be done to make filtering easier, but i think the version on salsa fixed the immediate issues raised here)
