First, Edboy, Pedro has the one-piece type quadant.
Pedro,
I don't quite understand why a flattened tooth in the same shape as it was designed by BSA should cause a problem. On the other hand, this is not an original part and, maybe, some small deviation from original is causing a mis-fit when the two gears come together. Maybe the flat tooth is landing on the tip of a tooth on the pinion and jamming things up. Now, with all that said, I still don't quite believe it is the reason for your troubles, but, I would think you could grind the short tooth to be a miniature of a pointy tooth with no harm. It might even help, but no promises.
Richard L.