The Nut in the Cellar
OK, first question. What is the brand and the finish of the poly you are applying? Is it gloss, semi-gloss, satin, or flat? The varnishes (other than gloss) have flattening agents in them and this requires the varnish be constantly stirred DURING application as the agents will settle out to the bottom of the can and leave you with varying levels of gloss. The flatter the finish, the more dulling agents, and the requirement for more stirring. It is also possible that the wood absorbed the finish unevenly and thus the variation. Did you sand between coats with 220, or finer, abrasive?