The Building Regs Cert should be issued by the Planning Dept or Building Control Dept of Council, depending upon what you've had done. The builder, again depending on the work carried out, can self certify some aspects of his work eg electrics. When the relevent depts of Council are satisfied that Building Regs have been adhered to, they will issue the Building Regs Cert. It should be noted, however, that these depts do not guarantee the standard of workmanship carried out. Unless they see something glaringly wrong, they will issue a cert. Their inspections, if any, are usually cursory.
I suggest you contact your local Council and discuss your problem with the Building Control Dept and/or Development (Planning) Control Dept. They should be able to inform you of any involvement they've had in your project and in the issuing of the Cert.
Should you remain disatisfied with the standard of work , I would recommend you commission an Expert Witness Report by a Chartered Building Surveyor. They charge approx £60-£80 per hr but are worth their weight in gold. They will inspect the work, report on defects, report on remedial work neccessary and will prepare detailed costings for any remedial works required. This Expert Witness Report is considered independent by the Courts and as such carries a lot of weight. Builders don't often argue with it!
Good luck.