Will the occurance of congenital problems increase due to advances in repair thus allowing faulty blueprints to be passed on unaturally?

Yes: This is evolution in the making, for better or for worse. It has been happening since the beginning of mankind. Basically, if a child is born with defects that make it unlikely for him/her to grow up, get married, and have kids; but that child is helped by his family, his doctors, and his community to grow up and reproduce; then he will be a great citizen but may also pass on his defective gene.