Sounds like the officials are not sure how to deal with your particular situation.
Are you sure the phills i presume the phill embassy in your country understand your already married? Im sure you told them but maybe they got confused. Otherwise it sounds like you will be going round and round in circles.
Also why do you have to have your passports in the same name?
Neither country as far as im aware insist that your wife has to change her surname to yours. If she can renew her passport in her family name i can't see the problem although im no expert on these matters.
