I do feel for the self fulfilling prophecy thing b/c our local schools do that as well: identify the high achievers early on and enrich them such that they later wind up identified as gifted due to their level of achievement while similarly able, or at times more able, kids who weren't achieving highly early on get left out b/c they weren't taught enough to perform as highly.
In regard to post skip experiences, our dd was at the top of the class in the grade up immediately after she skipped. However, she skipped much later in the game (5th grade) than your ds. I guess that, assuming the school did their due diligence in assessing him for a skip (his needs couldn't be met without the skip and they filled out an Iowa Acceleration Scale or at least did the testing it would require - IQ, grade level and above level achievement), I'd expect that he'd be rising back to the top of the grade within a year or two. If he is going to be undereducated until then, though, you may want to supplement at home for a bit to ensure that he has the opportunity to learn enough to catch up with the higher performing groups.
I believe that the general rule of thumb in skipping a kid is that s/he should be in the top 25% or so of the receiving grade immediately post skip. Do you feel that he truly is not at that place or just that they are underplacing him? I'd wonder about the latter b/c you mention him being in a reading class that is doing easier work than the group he had been in pre-skip.
