For what its worth, the last New Haven book seems to be heavily weighted toward the northern half of the New Haven market. Places where Hartford stations do well (Meriden, Cheshire, etc.). When compared with past performance, every one of the New Haven and Fairfield County stations did poorly in that book and several Hartford ones did very well. Both Hartford and New Haven are relatively small markets (geographically), so any inconsistency in the geographic makeup of the ratings survey is magnified.
You can't take too much away from 12+ ratings in that one book, which is what you're trying to do. How are they doing in the demos? THAT is the key question.
About the signal overlap, it really doesn't matter as much as you think. Each station still targets their home market and each one "sells" to advertisers in their respective home markets. As far as Clear Channel is concerned, the two stations might as well be 100 miles apart as neither has the ability to put a local grade signal over the entirety of the other's market. Or, put more specifically, KC-101 doesn't have enough signal over the entire Hartford market (the larger of the two) to be worth trying to rimshot Hartford (and pretty much ignore New Haven) with an alternate format. They can make a lot more money targeting New Haven - which is lucrative enough for CC.
Also, KC-101 competes in a different environment than does Kiss, so you can't just lump them together. KC-101 has to deal with the fairly strong hip hop signals that enter the market from Hartford, Long Island and New York - and with a very popular local urban/AC station (WYBC). The music and imaging have to lie between all of those. Kiss doesn't even think about that - they only need to concentrate on what WZMX, WPHH and (on the other extreme) WTIC-Fm are doing. This is why they sound somewhat different.
Kiss could target either market, but goes for Hartford because it is much bigger. No one targets the New Haven market from West Peak because they can target Hartford, where there is more money to be made.
In the end, with Kiss and KC-101, CC ends up cornering the CHR format (generally young females 18-34) in both markets with heritage signals. It's as simple as that. Frankly, there aren't many format openings left to flip either one to something else. If they're having issues it is because they are not running things well enough internally. That's what they need to work on.
Don't confuse radio (where Hartford and New Haven are separate markets) with TV (where they are one market).