I've done the same thing using my Dremel tool and an angled grinding head. I grind a spot on the back of the flint round just enough to allow it to fir properly in the jaws. With the larger locks on my kit guns though I normally don't have to do this, but for my Lyman flintlock I sometimes have to.If you run into flints that don't quite fit your lock ,here is a way to make alterations that is fast and easy. These wheels can also be used to re-sharpen the flat cut flints to a better edge than they had from new. I have some English flints that are too long for my lock and I just cut a groove in the rear to fit around the top jaw screw, works like a charm.
Here's what you need.