It's been a few months, but I believe that I had to call/email US Air to get them to add my Virgin number to a reservation. Even though I did that, I still hadn't received credit from Virgin a month after the flight, but after several emails I finally prevailed and got Virgin to credit miles and tier points.
Another little anomaly: On the Virgin site, under Airline Partners, US Airways, you may notice that no credit is given for discounted first class fares ("A" fares), even though these fares are eligible from other US airlines. I was able to get credit in the end, but maybe that was part of the problem!