Well regardless of making more or less power, short shifter or not, from my expierence it's 1 or 2 of the snycros that have issues first, then the others start to follow. Usually not as drastic as his case, but you never know.
Given the little info we have I bet it's a combination of some issue with that particular snycro, some missalingement of the shiter/linkage (whether from the stock parts that were never touched and/or the short shifter), and shifting hard into second gear more than others (on the road going from a light fast, you will start in 1st, shift to second and then you'll be going fast enough so you will let off and shift to a higher gear).
At any rate, if it were me, I'm wouldn't bet on the dealership being logical or fair.
They could even try to say that since it's modded he must 'abuse' it and it just happened to be the second gear that he abused first and that's why it's having problem. I'm more coming from the perspective that ansonivan is saying. I don't know the car, but generally speaking it's really, really, easy to replace an intake. 20 minutes=less possible hassle at the dealership.
If I were him I would go as much back to stock as humanly possible.