This sounds familiar. I was given some story by ICC about two month ago about not booking MNL ticket, it sounded like nonsense to me but your post suggests it may be true.

Anyhow PL is not the most regulated or efficient country in the world, I have been able to travel to and from MNL, esp on BMI Star A tickets and I never experiences any problems. In some ways its a fine place for a stopover although the city i such a sprawl it is well not to underestimate time to travel in a cab, although it won;t cost v much.