As Clacko said, the airline may have a significant factor (airline hubs) as well as the routing rules.

Since you're going through PHL and also CLT it appears you may be trying to fly US Airways to SJU.

US Airways has direct flights from both PHL-SJU and CLT-SJU so the chance the routing rules would allow someone leaving PHL to fly to CLT and then to SJU versus just to SJU might be slim.

Do you have the routing rules?

Have you tried doing a multi-leg segment using ITA?