This is a 3 day old private beta (elementary OS). Why is it changing the reputation of people (and therefore the order)?
Note that other tabs (e.g. month) are also off.
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As Kate Gregory already pointed out in the comments, a difference of 1 is already explained in Why is each rep off by 1 when sorting Users by year vs. all on a < 1-year-old SE site?.
There are two other issues you've uncovered here, though:
When you get the association bonus (+100 because you have 200+ rep on any SE site), these +100 are not counted towards the daily/weekly/monthly/yearly totals. However when a user's reputation is recalculated, the +100 are included in those tallies. Therefore, if a user has the association bonus, the difference between their yearly value and their total is
A point could be made for either of these approaches (including the bonus or not), but of course it should be consistent.
This answer is just a heads-up for you; neither of these two is fixed yet; I want to talk to Nick first what the best approach is to handle and repair these issues.