Well there's yer problem! [8D]

Feathers are going through the rest without nearly so much drag and interference as the vanes were having. With guaranteed 100% fletching contact, you can't reasonably expect feather fletched arrows to shoot exactly the same as vane fletched arrows. The two different materials don't react to contact anywhere near the same.

You also removed about 20 grains of weight off the tail end of the arrow and increased your FOC. Feathers will also cause your arrows to react a bit stiffer, but you've mediated that effect by going with shorter feathers with less stabilizing surface area, as compared to the 4" vanes. But those are minor differences, in the big picture.

I think the biggie is, you had the bow tuned with an old, worn out bisquit and now you've got a new one that's stiffer, with a round hole that hasn't been worn down and egged out yet. There's no guarantee the hole in the new bisquit is centered exactly like the old one was and, even if it is, there's no guarantee you got the new one seated in the mount exactly like the old one. So, most likely, the rest is holding the arrow a bit differently.

You can't reasonably expect to make changes to a setup and not expect to have to do some more work to make it shoot right again. You've got to retune.