Hi Nigel.
Although I don't process my own negs, this happens to me occasionally as well. To be honest, I don't think it matters which way round the negs sit in the carrier. I tend to put mine in shiny side up and "flip" and "rotate" the end scan to get it right way round.
Apparently, it is possible to get sheets of anti-Newton glass and just scan negs right on the scanner bed but that seems a bit radical. Then again, I don't profess to be an expert - I'm just happy with what my V750 gives me - even using the rather flimsy neg holders provided with it.
Paul.