I often read comments before noticing the unread count in the global inbox. Then I click on the stackexchange logo to see what's new and find the "unread comments" are those I've already read.
The best way IMHO to fix this is to mark items as read once you've viewed the page on which the comment was written. The obvious problem here is that viewing the page does not imply I read the comment. But I find with myself this is far more often the case then not. However, if you don't agree it should at the very least be marked as read after I make a comment in reply.