I'm pretty sure bullet size and weight are only used to compute the kinetic energy and power factor values for the output tables. My LR has been on 55gr .223 for ages and I've shot 45ACP on pistol and up to .444 Marlin on rifle and got good numbers.
First, I'd call or contact LR as they should be able to tell you what's going on for sure.
I have had a few instances where I got crazy high numbers, and low numbers as well. I attributed it to being too close to the LR, and maybe the LR was picking up the gasses. Most likely it has to do with muzzle (or muzzle brake) relation to the LR. You prob need to be either further to the side, or more in front, or both. Are you using a suppressor? What gun are you shooting? It could also be that the LR isn't aimed at the target, how are you aiming it?
Oh, I also thought when I got high/low numbers that my tripod wasn't steady. Make sure your gun isn't rocking the LR when you shoot. Any movement of the LR with muzzle blast would probably give screwy readings as the bullet is going one way, and the LR is moving another..