Disclaimer: I don't know for sure how the algorithm works, this is just my guess from what I've seen.
For comments: you can see if your upvotes are being counted by looking into the user's karma. You can't give lots of karma to one user though. After a few upvotes to a single user, the system will stop recording them. I guess this is a way to prevent karma inflation, and a group of friends cheating themselves into lots of karma.
Again, only a theory, I mean nothing by it.
We get to look into the source code to see what is really happening.