Can't comment on the specifics of why the 4 blade is flying better than the 3 blade, but that the 3 blade is flying differently at all suggests a couple possibilities.
1. That particular arrow isn't straight
2. The broadhead isn't centered........did you spin test?
3. You have less than perfect arrow flight, regardless of a good paper tune.
I too had bullet holes with field tips and although this helped me set center shot, when I screwed a broadhead on I was hitting 4" low at 30 yards.
I used this Easton photo to eliminate the less than perfect arrow flight and now field tips and broadheads are hitting the same up to 50 yards, my last shooting range.
