Thanks for the details, makes working with something like this a lot easier. So a few things right off the bat:
-I have had issues with RPGMaker when the game directory is placed too deep in other directories. Not this issue, but it really doesn't seem to like that. So for testing it may be worth moving the game directory to be right on the root if it isn't already.
-Keep in mind that when you FIRST start the game, none of your stats in the menu will reflect your stats from the first game, because of the time skip. It hasn't happened yet. Wait until the SECOND time you enter Haven, then check your stats Status--->Subject Stats. If they're all still zero despite having numbers in the file, yes, that's something breaking.
-You said you've already tried messing with the data values, but to be clear, to trigger the extra scene you need "NumberofBoarDefeats" to be 3 or higher (Unless I've messed something up, SHOULD be three though, and no penalty to setting it higher to be sure.) Then walk past the alley by the hotel, again, SECOND time arriving in Haven.
I'd check Subject Stats as your main diagnostic check that the data is getting through, again, after coming back to Haven the second time. Might also be worth moving the game to a main drive to test, though I can't imagine why that would cause any issues. Give this first stuff a quick check, and if that doesn't do it I'll have to dig deeper, though it may have to wait till after the content pack is out.