Are you shooting a whisker biscuit? If so, you may find that you need to move the rest towards where the bare shaft is hitting on the windage adjustment if the bare shaft and fletched are not hitting together..
I have/have had 4 different bows, all with WBs. (one dual yoke/dual cam, one hybrid with one yoke, two binaries with no yokes). For all 4, I had to move the rest in the direction the bare shaft was hitting. The last one I finished dialing in today, having just bought it as a bare bow. When I walk back tuned after getting the bare and fletched close at 20yds using both fletched and bare shafts from each spot (about 10 paces between shots), the fletched moved to the right and the bare moved to the left as I moved farther back. I moved the rest to the left less than 1/32" and they all came together in a straight line.
So, if moving the rest one direction doesn't work, try moving it the other. Just move it in very small increments each time, because it is really easy to overshoot the sweet spot.
Realize moving the rest is just one way or just part of the process in skinning this cat. If you have yokes, they may be the solution if moving the rest doesn't work, or if it ends up way off factory recommended center shot. Shimming the cams and adjusting how far in or out the cable slide is are other methods used to fine tune.
Before walk back, set your sight dead on windage-wise. If when walk back tuning, the fletched and bare shafts are hitting together but the line looks slanted, check that the 2nd axis on the sight is correct before messing with the rest.
As stated above, you must have very consistent form for the bare shafts' points of impact to have any meaning. If you are consistently getting bullet holes through paper when close up, sounds like your form is okay.
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