Hi Joe,
The automatic route determination in sales order happens as follows -
1. The system reads the departure zone from the Shipping point
2. Then it reads the receiving country/zone from the Ship to party customer
3. Then it reads the shipping condition from Sold to party customer
4. Then it reads the transportation group from the material master
If any of the above fields are not setup properly, the automatic determination won't happen even if you have defined the routes correctly.