This actually sounds like a potential cause for this glitch, but not a justification.
I'm not a Diamond but I've noticed that I am always short points when I book a rate that includes breakfast (like the AAA Breakfast rates they have a few times a year). Of course, like your experience, the amount that is short is always different.
You know, I've noticed that a few times, when booking breakfast inclusive rates for $X, the rate is listed in the expense summary on my folio as some number smaller than X plus a breakfast charge. I can't remember specifics, sadly, but it jumped out at me as I suspect it could cause some folks issues with their expense processing. ($X is always less than the standard daily rate without breakfast.)
I'll try to look through my account and see if I can find an example.
As for the variation, I wonder if it has to do with whether the charges were removed manually or automatically on a given day?