Primary Emails not Being seen as primary
I found a solution to this using the 'Update Multiple Contacts' feature. Here are the details:


I created a profile to be used for search views that contained the Org name and Email (main).
From search results I selected the Org that the primary email was not showing and selected 'Update Multiple Contacts' from the action menu.
I  selected my newly created profile for updating email.
When the update screen loaded I just hit the update button and this updated the main emails to be primary.


Since this was a relatively small amount of records this solution was manageable. Probably not the best solution for a larger amount of records.