It's a known "limitation" for most big boards. Many end up hacking showthread.php a bit to avoid it, because basically what happens is it has to count the number of posts in that thread every time when handling the pagination.
Some sites split their threads after 1000 or so replies, just for efficiency sake. If this is too much of a hassle, then you'll have to dig around for some of the optimization threads here. I remember a few detailed ones, but you're on your own finding them. Maybe someone else bookmarked them. Should be on vb.com, as well.
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