My recollection with calluses was in the beginning I developed small blisters on my finger tips. I laid off guitar for a few days an they eventually turned to calluses. Those calluses eventually peeled off but the skin underneath wasn't anywhere near as tender as starting out. When the blisters formed, it was AGONY to play.

Something else that may be going on is that you are overcompensating slightly improper finger positioning with extra pressure of your fingers. This will work itself out over time. Try taking a real hard look at your finger positioning and see if you can determine a way to fret the problematic notes with slightly different finger positioning. We are talking about micro-adjustments.