It appears that incoming messages to Outlook are not being run though the rules list. The result is that some messages designated to go to the inbox by a rule are not going to the inbox but rather to the junk folder.
Then when going to the rules manager and running the rules the proper action does take place and the desired messages are moved from the junk folder to the inbox folder.
In short the desired result is achieved by running the rules manually. It would be a better result if the rules where run on incoming messages automatically rather than having to be run manually in rules manager.