There's definitely some confusion here, ending 31 is the "good" ending for Keir's second chapter. There is no other ending to look for. As for the weird behaviour from the game, there's two possibilities I can offer:
1) Ren'py did something weird. It's rare but not impossible for the engine to have a major hiccup and behave unexpectedly, in which case starting a fresh playthrough and skipping through the early material should put you back into the normal gameplay.
2) You finished Chapter One with less than four affection points with Keir. It's impossible to score enough affection points in Chapter Two to get the last CG and the kiss scene unless you already have four points when it starts. Keir's good end in Chapter One only needs three affection points, so it's possible to get locked out.