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All chkrootkit does is check those ports for a listening service, as they are (were) typically used by the "nasty" it is checking for.
You have portsentry listening on them (which you have presumably set up to do so) so there is no problem.
6667 is suspicious as an irc port, as is 31337, (but maybe not for irc activity)
If the processes are not running, the lsof on them will return nothing.
If they are running, or recently run. lsof will show you what files started/used them.
if descendant is right would be nice, then my question is: is it possible that what rkhunter detects is portsentry listening to the ports or is it something else? sorry for my newbie talk :P
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