I've suspected for a while that downvoting imposes a limit on one's daily reputation limit and therefore counts downvotes twice. Today with TheTXI's help I was able to confirm this.
The daily reputation limit is calculated by (200 - (number of downvotes)). Not downvotes you've received, but downvotes you've given.
For example, let's say this morning I give out 5 upvotes and 5 downvotes for various questions and answers. My rep drops from 5000 to 4995 because of the cost of downvoting. Then I post a great answer that receives 20 upvotes. I receive 195 reputation (because of my five downvotes). Now my reputation is 5190.
It's counting downvotes twice. Once immediately, and once with the daily cap, preventing me from getting those last 5 points even though I was upvoted enough times.
TXI and I tested this in this way: I downvoted him once I was at my rep cap, then he upvoted me. He expected my reputation to go back to what it was (with his upvote restoring one reputation), but it was not restored.
As someone who both downvotes and reaches his daily reputation cap often, I'm missing out on a lot of reputation I would have otherwise gained. Plus this calculation makes it more difficult than necessary to determine if I've reached today's cap yet or not. If it were a constant 200 I'd just be able to look and see if I've hit 200 yet or not.