Update:

Just got this reply from AA:

Dear Jacobin777,

"Thank you for your email. We have identified and resolved the issue. Although you will not see any changes to the points that have already posted you will notice on 6/22/2015 a 'Base Point Adjustment' for the remaining points was added to correct the point calculation error.

We apologize for any inconvenience and we appreciate your support of the Business Extra Program."

I did see an adjustment to my account.