Not all votes are counted, and not all votes that are counted are displayed (for instance, when you downvote someone even if they are at -4 the votecount seems to be stuck at -4 but the karma of the person is still decremented).
This question and a bunch of others I've written up in this article: http://news.ycombinator.com/item?id=1755533 .
No, then it wouldn't be secret anymore.
Security by obscurity is not perfect but in this case having that knowledge out there would only benefit the spammers and the 'gamers'.
Is news.ycombinator.com open source ?
Yes it is, the code is written in a language layered on top of scheme called 'Arc', you can get the whole package here: http://arclanguage.org/ , the package includes a slight variation (the 'secret sauce' is missing) on the code running HN.
It redirects to the login form, and then when you return, the up-vote arrow is gone but the vote isn't counted.
It also happens to me when up- or downvoting comments.
I think there are safeguards in place to prevent us from voting too rapidly. E.g. when I go through a thread and "adjust" it to my liking (up/down vote as I see fit) and then reload, then usually half of my votes didn't make it.
I'm trying to get into the habit of voting immediately, but keep falling back to "buffered I/O" when I'm not paying attention...
Although of course I did not answer the original poster's question, don't you agree it is a bit humorous that by trying to answer most people probably will try to vote up to check if they have the same problem?
There's perhaps even something to learn from that.