It COULD be your rifle. CCI primers are pretty tough, that's why Lee says to use ONLY CCI in their priming tool. It is just possible that the Winchester rounds you fired had "softer" primers than those CCI's. Unfortunately, you can't really decide this by examining primer indentations in primers when the round fails to fire, since the indentation doesn't generally look the same as it does if the powder charge fired.

Try some "softer" primers like Fenderal 210's, and see what happens. (I have never had a CCI primer fail to fire, but most of my most accurate loads have been achieved with Federal primers- most, but not all.