Virgin Atlantic Flying Club - Redeeming VS miles on US

I called VS to do a domestic round trip on US: BOS-DCA-GSP, GSP-DCA-BOS. They said it would be 50,000 miles because it's a connecting flight. Only direct flights are 25,000. The VS agent called US twice to verify this. Seriously? Ended up booking using 20,000 US miles thanks to the Barclays discount.

I have found that 1 mile does not equal 1 mile.
Whilst the earning of miles is much the same across airlines the spending differs a lot. It also seems to depend, sometimes, on if you redeem on the earnt airline or a partner airline.

Last month I wanted to go NYC-HKG (via LHR). With Virgin miles it would take 180k roundtrip. I booked using Continental miles - 120k roundtrip - but it was still all on Virgin (as a codeshare). Earning miles on VS and CO is equal for me so the value of the CO miles must therefore be greater than VS ?

Sure, I agree that CO miles are worth more than VS miles. Only reason I have VS to begin with is the Bank of America card. But has anybody else booked US flights using VS miles and been told they can't have a connection?