Are your arrows numbered/marked individually? Have you spin-tested the arrows as well? You may have sporadic flight with certain arrow/head combos. Mark them individually and then shoot. If you have a "flyer" try a different broadhead and see if it hits the same place and then put a field-point on and see if that arrow still hits different. What you're trying to do is to eliminate "bad eggs". Form issues, i.e. torqueing, will also cause what your describing.
As far as fletching goes, having the blades match up with fletchings isn't going to hurt but honestly with todays technology and improvements it isn't a requirement like it was years ago. Also, having more helical/spin in the arrow can improve arrow flight and consistency, but it will also increase noise and have a slight reduction in speed. Most of the time, a slight off-set helical is sufficient.