I thought the association bonus wasn't supposed to be counted in the specific time frames; however, after looking at the code, the 100 point association bonus is supposed to be counted, but the starting 1 point is not.
For some users, including myself, the association bonus isn't counted for some reason. It must be a race condition based on when those values are first calculated for each user, but I can only guess as to the specific cause. The temporary solution is simply for reputation to be recalculated on the affected users, and there's a relatively easy way to do that. I tried this on my local development environment and it automatically corrected my rep, so I'll talk to someone about getting that fixed in production. Perhaps someone on the core team will also have an idea as to what's causing it in the first place.
The rationale for why the starting 1 point is not included is that it is not really a reputation point, it's simply a minimum value and what our reputation counter starts at (instead of zero). It has no date associated with it - it's not even in the database - and therefore isn't considered part of any date range.