A 13 1/2" sett is a huge sett and generally requires "cheating the pleats" in order to get a reasonable number of pleats into the kilt. If you looked carefully, you'll probably find that the shallower pleats are less than a full sett apart, and the occasional big one is a full sett. It's generally unavoidable to have a few really deep ones. As long as the reveal is even, you shouldn't worry about it. It will never show from the outside of the kilt, even when you're walking.

Having said all this, it does seem a bit odd to me that this is true for only one of the kilts. But, it can happen, depending upon how the pleats are chosen!

Barb