I know exactly what you're talking about.  The problem is that the tool you're using is only deep enough to accept the sight post in the center (if you look inside the sight tool, you'll see that it's concave, not flat).  The fix is to get a drill bit that fits the hole in the tool, and drill the tool all the way through.  I did that with a couple of sight tools, and now it's VERY easy to adjust the Trijicon sights.

There is also a long, narrow sight tool that is already deep enough, but I already had several of the short, fat ones, and they're easier to use overall, so modifying them was easier for me, and turns out to be a better tool in the end.

-Troy