If you weren't at the board while the threads were "alive" (read: still getting frequent replies), you only got one email for each thread that was posted to. It doesn't email you again for each thread until you visit the board again. But if you're actively visiting the board at the same time a thread you've subscribed to is actively being posted to, that's when you get the shitloads of emails. I'm going to try to find a way to implement a no-email subscription system but depending on how close vBulletin 3 is to being released I may just wait it out (the vBulletin 3 conversion will be enough work itself, one more hack won't be worth it if it's only x days or weeks away)
Additionally, you'll only get emails for those threads which you selected to subscribe ("Subscribe" on the quick reply or "Email notification" on the full reply, or by clicking the "Subscribe to this thread" option down at the bottom without replying)