the masks on my 645 have a milled step / slot for the negative to lay in
I just looked at the carriers on my De Vere - this is not what I see on the original manufacturers parts. However, the top (silver coloured) side of the "bookform" glassless carrier has a slightly thinner milled area next to the cutout on its top side. This is meant to reduce reflection from the vertical inner edges of the lit side of the carrier. The top and bottom plates are joined at the back with two small flexible-plastic hinges.
Going from the top, when ready for use, I see the silver plate with milled area uppermost, then the negative between the two smooth sides of the carrier-plates, then the smooth lower plate, then the main part of the negative-carrier with the masking etc.
Is it possible that your plates have become separated at some point and that the upper (silver coloured) plate is now upside-down ? That would take the weight of the head off the negative and it would no longer be held at all flat.
Alternatively you may have a carrier intended for holding mounted transparencies or even a part of a pin-register negative carrier in some sort of "Franken-carrier" arrangement.