Are both of them newer-model (production year 2001 and later) BT-99s (which I believe are all constructed as extract-only)?
I think one of your BT-99s is simply lifting the shell further out of the chamber than the other BT-99 does. I'm working on memory here, but the reason for this is, I beleive, that at some point in production, Browning changed (slightly) the dimensions of the extractor and extractor extension due to just such a complaint as yours. I think the most recent production run lifts the spent shell a little higher than earlier guns. We're talking only about 0.1-inch difference (maybe less), but it does make it easier to grasp the head of the spent case.
Do a close side-by-side comparison of both your guns and let us know if you can confirm a difference in extraction height. So, there might not be anything "wrong" with either gun . . . it might simply be two guns built on different sides of a small design change.