Here is some data on primers and primer pockets. If you take the middle of the tolerances, you can figure out how deep the primer should be sitting (essentially flush):
http://ballistictools.com/articles/primer-pocket-depth-and-diameter.php
A more likely scenario is the primer is minimum and the pocket is maximum and the depth will be 0.008". Some measuring of the actual condition would be useful.
You simply can't reload bottle-neck rifle without a case gauge. There are more precise tools but the gauge is the absolute minimum. If I had to bet, the shoulder is too far forward and, if I were doubling-down, I would bet the die isn't bottoming out to the point of the press camming over while the case is resized. But I have been wrong before...
That shoulder location is critical. Too short and there is a possibility of case head separation. Too long and the round can jam in the chamber. The case gauge tests both possibilities and it checks the brass overall length as well.
Are you using an RCBS X-die to control neck extension or are you trimming to length? The case will always grow when resized unless expansion is controlled by something like the X-die. Even with the X-die, you have to trim once to minimum length.
I guess before we can provide any definitive recommendations, we need to know a lot more about your process.
Richard