I assume you're working on a coupe...
One of the biggest suppiers for that window channel is
Auveco. I've looked through their master catalog and have noticed they manufacture more than one size of that shaped rubber channel.
It seems
that shaped channel was used by various other car makers over a realatively broad range of years, with subtle changes in shape or size.
Auveco would not have one box marked "Model A" ...instead each box will give exact dimensions and a corrosponding part number.
I wonder if there's a chance that Model A supply houses are shipped different shapes/sizes by whoever happens to be the warehouse picker that day?
http://www.atrim.com/Page153.html
My "second hunch" automatically defaults to offshore quality goods.
This has been flogged to death, so I'll leave it there....
For a remedy which should seal your existing setup...
you could obtain a roll of 1/16
or 1/8 x 1/4 black butyl glazing tape at a local glass shop.
....the old glass guys call it "40-40 tape"
Take out the window and press a bead (just like bubble gum) around the inside of the painted window opening so it follows the edge. Make an overlap join at the top.
Next tighten the window & seal against the soft butyl so it gishes out. The excess can be trimmed off with a popsicle stick ...with some stick trimming & practice you can cut a perfect edge by holding the stick just right and the wood won't mark your paint job.
Some benefits of using butyl on your vintage car is:
-it's what they used in the day
-it softens and reseals itself on warm sunny days
-it leaches minute traces of harmless oily residue into surrounding metal which is a wonderfull rust deterant.
It's wise to avoid silicone sealant which does the exact opposite and
promotes rusting of bare metal, especially deep within cracks and cavities of the car body.