I get a slightly different problem.
When I submit a confirmation email (Gallileo) from our work travel agent it creates DJ flights as VA (not sure why, as it has the DJ flight code in there) and that means that Trip It Pro doesn't monitor the flights.
So I always submit the confirmation (so I have my hotel in Trip It) then I delete the flights, and resend myself a confirmation from the Virgin site for the flights, then forward that to Trip It.
Bit painful but haven't got anything else to work.