When looking at what you can do to stretch out a ticket to maximise the TPs you are restricted to what the ticket will allow. Each ticket is based on something called the Fare Basis or Fare Rules. Once you have chosen your flights in Matrix you get the final price and at the bottom, where it says "How to buy this ticket" there is a link to the rules. In there are the limits and restrictions for that ticket. For the OTP-PHX tickets at that time I notice that it says
Category 9: Transfer restrictions
2 TRANSFERS PERMITTED IN EACH DIRECTION FREE
1 PERMITTED FREE BETWEEN AA AND VY IN BCN/ROM IN EACH
DIRECTION
NONE PERMITTED FREE BETWEEN AA AND VY IN EACH
DIRECTION
2 PERMITTED FREE IN EUROPE IN EACH DIRECTION.
AND - 2 TRANSFERS PERMITTED IN EACH DIRECTION FREE
1 FREE BETWEEN BA/IB AND B6 IN BOS/JFK IN EACH
DIRECTION
1 FREE BETWEEN AA/AY/BA/IB/US AND AS IN LAX/PDX/
SEA IN EACH DIRECTION
1 FREE BETWEEN AA/AY/BA/IB/US AND AM IN MEXICO
IN EACH DIRECTION
1 FREE BETWEEN AA/AY/BA/IB/US AND AC IN CANADA
IN EACH DIRECTION
1 FREE BETWEEN AA/AY/BA/IB/US AND HA IN HAWAII
IN EACH DIRECTION
2 FREE ON AA/AY/BA/IB/US ONLY IN EACH DIRECTION
FARE BREAK SURFACE SECTORS NOT PERMITTED AND
EMBEDDED SURFACE SECTORS PERMITTED ON THE FARE
COMPONENT.
Could this be the issue?