your son is born in Ph therefore he is intitle to get a philippine passport believe me ive been through on that problem as well..i got my son as well..he has both passport PH and English(he was born in the Philippines).. so when you apply for his passport just show the birth cert from NSO and some doc they needed from you as mother..do not relay on Bureau of Immigration ..deal with DFA..thats all..am sure your son will be fine..they just want to make money out from you thats the point why they delay

btw reading your thread again you should have get his PH passport before the English on that way is much easier to deal with gov and immigration itself coz the showing the PH passport itself to them they wouldnt have reason to delay whatever is your purpose to them
as my experience when i deal with the Bureau of Immigration before we come to UK..ive told them my son got an English passport do i need to pay any tax?? and they said yes..but i oppose saying .."but my son is filipino he is born here and i got his birth certificate" and filipino passport ..then ive seen them speechless lost of word..and one man say ahhh..oh i see ..his fine then he dont need to pay anything...if he got both passport..so therefore the only trouble is if you only declare english passport without PH that they make money out those people who wont bother to know there policy..
hope that help and Goodluck