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 think the SBI lab got the results correct the first time. Nifong just couldn't believe it and wasted the taxpayer's money on a "better" lab. He was so sure the LAX players were guilty that he bet a lot of money that the SBI lab was wrong, an he lost.
There is no way the SBI missed the DNA from the boyfriend. If they did, then we need a new SBI DNA lab.