No Middle Name in BC but w/ Middle Name in all records

Hi! I have a problem in all my records because I am an illegitimate child because my parents lived out of marriage and they already deceased so in my birth certificate I don't have a middle name.. the problem is, in all my records like school credentials, employment record, and all government agency's record like TIN,SSS,Philhealth,and Pagibig I have middle name used because When I was young and start schooling, they require me to have middle name so I used my mother's maiden middle name ever since. The problem is I have to take board exam.. my credentials and birth certificate conflict... what should I do?
I want to fix my birth certificate to parallel with my records. is it possible? as explained in memorandum circular no. 2007-005

The law recognizes that middle name is not required for an illegitimate child.
There are two approaches, correct all you identification deleting your middle name officially and securing a new identification card and credential without your middle name. This requires submission of Affidavit of Discrepancy and some documents to the various offices. Requirements may vary depending on the institution.
The other one is just to check with the admin of the board exam the acceptable credentials and limit the presentation here.

There may be other ways. Are you male or female?

Thanks for the info
I am a male.
The scenario is this;
Last last week I called NSO customer service and I asked about the proper way of arranging my birth certificate, they said that I have to fix it to the municipality where I was born, bring necessary documents that proves that I used the said middle name.So I went to the civil registrar of municipality where I was born...They said it is okay that I don't have to used middle name since I am illegitimate or I can used the surname of my father because he recognized me as his son because he signed my birth certificate, BUT I don't want to. I want to used my mother's middle name and surname.
So the head of Civil registrar look for memorandum that I should not used the middle name of my mother. Accidentally she showed me the Memorandum Circular No. 2007-005 (c) signed by Carmelita N. Ericta that explains that I could able to used my mother's maiden middle name. How's that???