I know there are minor differences between votes sum and reputation, like the fact that no user can have negative reputation. However, the sum of the up/down-votes and bounties differ from the reputation very much (both positively and negatively), see here.
What am I missing? Surely there are some other things in effect, but what would make changes in reputation as large as ten thousands?
Edit: Thank you all for suggestions, daily reputation cap was the thing that generated the biggest differences. An improved query can be found here. Of course, if you would have some further suggestions, go ahead.