Why are there sheen differences between woods?
I hate to be critical of other contractors, but from the clues you have given in your question, I think I know what happened.

First, pine is a much softer wood than oak and needs to be sanded very smooth before the first coat of urethane. The first coat raises the grain of the pine and almost always is somewhat rough regardless of how good the initial prep was. The first coat is sort of a sealing coat and must be sanded lightly to smooth it for the second coat. If the first coat is not fully cured and sanded, subsequent coats will only exaggerate any flaws or roughness. This is what I think happened when you noticed the roughness. 

As for a difference in sheen. If the contractor applied the same urethane, semi-gloss for example, the sheen should be pretty much the same as it was before the 3rd coat. They may have used one grade lower sheen. Satin instead of semi, or semi instead of gloss.  If you can see any noticeable unfilled sanding marks or really thin coverage, then perhaps the rough surface was sanded with a very fine paper and not over-coated. Oil based urethane stays tacky for several hours. At best conditions, it could be dry to the touch after 2 to 3 hours.