Here is another one I have dealt with in the US that is headquartered in Malate, Manila.
http://happysun8.com/HappySunTravel/Contact.html
Again, I have only dealt with the LA office so I can't vouch for their Manila operation.
+63-2-400-5901
I have been wondering myself what kind of fares I can get ex-MNL instead of ex-USA so I wish you luck on your quest.