I was wondering how the SBI could miss that. So let's assume they didn't. Why, at that time, didn't Nifong go out and get Crystal to ID the three guys it could be? Why wait for the second DNA?
I think Nifong asked her about the other sources of the semen as soon as the first results came in. Since the nail DNA was "inconclusive" he was able to use that as his excuse to send the samples to the private lab, keeping hope alive in Durham that a match could still be made.
Meanwhile, he had the boyfriend "swabbed" on May 3, the day after his primary win. No coincidence imo. With win safely in hand, he sent the new swab, and I presume those of the two "drivers", to be examined in a "rush" job allowing those results to come back with the original 46.
I don't think he did wait. He got the samples from the three and sent those for testing to the second lab along with the additional testing request done on the fingernail.