I think your problem lies here, from the help file:
Show whois in active window
Shows /whois results in the channel, query/chat, or custom windows if it is turned on and if a /whois is issued inside one of these windows, otherwise all /whois results are shown in the status window.
When the /WHOIS command is sent, it's not being sent from within the channel and as said above if it's not being sent via the channel, query/chat or custom windows results will appear in the status.
-Andy
