Score refers to the sum of your vote scores on posts, which is the upvotes minus the downvotes. That is, suppose you have 3 answers to questions under a specific tag in one day. The vote distributions are: 12/0, 8/-2, 16/-4. Then, your stats for that day's activity in that tag is:
- Reputation: 200 (cap'd!)
- Votes: 42 (12 + 0 + 8 + 2 + 16 + 4)
- Upvotes: 36 (12 + 8 + 16)
- Score: 30 (12 + 0 + 8 - 2 + 16 - 4)
This is always the case whenever the system uses score. Users might refer to "reputation score" or "reputation points", but in the system, score will always be specifying the value of your vote score across posts. That makes it not synonymous with votes or reputation, but rather a measure of the net votes you've earned.