Hi there
I travelled in the USA earlier this year on V Australia and Virgin America, though my flights were booked separately.
While the V Australia flights came through as expected, the Virgin America points took about a month and a bit to come through, and they had everything correct. I'm sure I still have the boarding passes somewhere, but I'm pretty sure that it had my Velocity number on it (I think it had DJ <Velocity Number> - but I could be crazy
)