I would not expect bench resting to give the same poi as freehand, nor would I expect freehand single handed to give the same poi as freehand double handed. Recoil reaction is not the same when holding differently.
You might be flinching it low, and as advised the exercises already described will help you to identify and avoid that, but don't get hung up on the bench rest results. Adjust your sights so that poi is where you want it using your chosen poa. Use the exercises, and, as your group size reduces you may find that you need to tweak the sights - concentrate on small groups not on poi - with a small group a simple adjustment of your sight will put them where you want them - with a large group no amount of sight twiddling will achieve the result you are looking for.
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TANSTAAFL