When I used it, it seemed to me that the rust converter had to really mix well with the rust - i.e. thicker layers of rust will not get the converter in contact with anything but the surface stuff. Add to that the fact that it tends to form a black primer substance, and it becomes even more difficult for the liquid to get in contact with deeper rust.

You should probably remove most of the deeper rust before applying the converter - it works really well on surface rust.