Your problem is why I try to avoid cutting crimp grooves for levergun cartridges. The throat vary so much, and change with use, plus the variations in brass as you've encountered, make it near impossible to cut a crimp that is perfectly placed.
Try seating without crimping, until the rounds chamber with light lever pressure, then factory crimp lightly. This should solve the problem. The only reason for crimping rifle cartridges is to prevent bullets being pushed deeper into the case. With lever guns this is normally caused by the stack of cartridges slaming along in the magazine. A light crimp fixes the problem.
If crushing the Lee Factory crimp in makes the bullet move forward a little, because it is only catching the edge of the crimp groove, seat a bit deeper as needed so the crimping brings the bullet out to desired length.
In my experiance, most rifles, of all chamberings, have chambers cut way longer than the sami specs. I always leave my brass long if a throat slug indicates there is chamber room for long brass. Sometimes there will be up to an eighth inch of space ahead of the case. Even 1/16 inch gap between brass and beginning of throat can allow lead bullets to obturate out into the gap and damage performance, IF THE LOAD IS HEAVY ENOUGH TO OBTURATE THE BULLET.
Try the above solution. Since I recommended the crimp groove, if it doesn't work, I fit the mold into my trash basket and make you another N/C.