I had the same problem with mine, even after bolting down (I thought that would be the fix). What I found after spending a night capping empties and going through a bag of caps, is that I was trying to hard to counter the effect. I was either pushing really hard down w/ the handle, or grabbing the red plastic part that the capper is attached to from the back and pushing forward.
I found the fix to be not trying so hard when capping, and just pushing down quick w/ the capper. It seems that trying to increase capping pressure was partly to blame for my caps coming out uneven.
Starting w/ a centered cap and bottle definitely helps, too.