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Why do comment counts often disagree with what I see?
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because when you load any page listing posts, you don't want your server to have to go and download the actual entire comment thread for every post that is listed. And then have to go and count how many there are.
Because it would be slow, especially with multiple servers involved. Every time you loaded your home page or a community the server would have to start from scratch gathering the data. It would be more accurate but it would be very hard. And not give a lot of extra value.
So it's more efficient to have a piece of data attached to the post that just reports the number of comments. Same way as there is a piece of data that contains the title, the name of the person who posted it etc. And that value is updated in some way. Apparently in a way that has not yet been perfected. :)
I appreciate your patience, I updated my previous comment, I think I finally get what you're saying.