In the well L96 (mb01, mb08), unlike the VSR's, the mag catch is fixed to the outer barrel, so it should keep the magazine in the same position relative to the chamber. Therefore, the height of the magwell in the stock shouldn't affect the magazine's position.
There's probably something wrong in the assembly of the gun, wether it's the stock itself or the receiver to the stock.
You could try assembling the gun without the cylinder and looking through the receiver in direction to the barrel, with the magazine in. You should be able to see the top of the mag and the bb's loaded poking a bit through the hole in the chamber where de cylinder head nozzle enters. It should poke the same amount on both receivers.