My guild (Pro Bowlers) has experienced something similar (which you apparently also have noticed, so you have quite the eye my friend). A few weeks ago we had 54 points; won the challenge; and then had 48 points. It was at first irritating, then we realized that just means more "easier" challenges, so it had a silver lining to it. Even more recently, we went through a very cold spell and had 51 points. We lost three in a row, and then had 54 points.
I can say with certainty that we have gained points from losing, and have lost 6 points for winning. There is no logic to any of that, and I don't even bother trying to muse over the "how can this be?" conundrum. I've played Sublinet games (as have you) for way too long to be surprised by anything anymore. You always think you've seen it all......until the next thing that happens that you never saw before.
Anyway, I have no answer, you will obviously get no answer (which I'm sure you know), but you are not alone in witnessing this stuff, nor are you losing your mind!
Hope all is well with you, Ashley. It's awesome to see Rebels right up there representing the non-squiggly lined speaking people of the world!!
-Jem-