how to process outlook rules on Lync IM missed conversations

Outlook (at least the 2007 version) will not process rules which might run against Lync IM "missed converation" messages for some reason - probably because it doesn't see them as "incoming" messages and rather "stored" messages.  If you manually run the outlook rule it will process those messages.

So a round-about way of having outlook process rules on those types of messages is to run these rule via a VBS script run by the a scheduled task in windows.  The VBS script you're looking for is here:
http://www.windowsreference.com/ms-office/how-to-schedule-outlook-2007-rules-to-run-at-specific-time/

for constant, UNREAD_MSGS_ONLY see below
'Name Value Description
'olRuleExecuteAllMessages 0 Executes a rule against all messages in the specified folder or folders.
'olRuleExecuteReadMessages 1 Executes a rule against messages that have been read in the specified folder or folders.
'olRuleExecuteUnreadMessages 2 Executes a rule against messages that have not been read in the specified folder or folders.