I use a Jojan Multifletcher. Firs thing to check is the reference point on the clamp where you place the rear of the feather. Are all the notchs the same distance from the end of the clamp? If you use a different reference point (ie a sharpie mark, or "scratch") , are they all uniform?
The second thing to do is to make sure your nock rings (index rings) are set at the same distance in the frame. There should be a finite retention detent which keeps it in place. If you have a weak spring, you can easily push the index ring back, changing distances.
Third: be careful placing/holding shafts in place while applying the clamped feather in the glue process. Sometime the shafts slides forward a bit as you place the clamped feather on the shart-creating variation.
Fouth: If your nocks have various "tightness" levels, you may not be seating them fully/uniformly on the "cross bar" inside the index ring. Also, related to earlier point, hold the index ring solid as you place the nocked shaft into the index ring-while seating the shaft. This force can make the index ring slip out of the index detent. All creating variation of depths yielding variation in fletch position.
The last thing I do before I put glue on the clamped feather, is to push each shaft into the index ring-with my other hand/finger on the outside of the index ring (so the force doesn't push out the ring). Then I check for shaft marks in relation tk the upper frame of the Johan. This gives me the "all clear" to place the clamp. I will also repeat this "shaft stuffing" step on the just-glued / clamped shaft. Then I move on to the next shaft. Wash, rinse, repeat....
Place all shafts/nocks in index ring, and then LOOK at the higher end of the JoJan frame and the shafts. Are they all aligned in the same position? You can generally pick up some reference point if there are graphics on the shaft. If not, make a mark on the shaft where the upper/higher side of the frame is, so you do have a "reference point". ie, use silver Sharpie ring/mark around the shaft, or piece of tape/wrap, or paint. If you see variation from the frame/reference mark on the shaft, something is not position properly/uniformly.
In short, just double check for variation in things that move or place things (clamp reference point, index ring, nock seating and tightness etc).