I think you are referring to Non-stops btw PHL & IAH.

Direct flights (as you refer) are flights with the same continuing flight # via a connection.

I see 3 non-stops btw PHL & IAH on the Dec dates that I pulled up. If these times aren't convenient then you will need to make a connection, but be careful if the flight # remains the same all the way from point A to point C thru point B you may only receive miles for point A to point C, and not for the round about way for 2 flights.

As to why they are doing this --- "Only the Shadow knows"!!!