I never had this before (and using WordPress for more then 4 years now) but i think the_content is wrecking my loop!
In my index.php i just run a simple loop, a default one, no strange things at all.
But when i try to limit this loop to 2 posts per page with:
it shows my first post twice and then it just loops on and on, so it doesn't listen to the query_posts.
If i remove the_content(); from the loop it runs fine! When the_content is in there it goes wrong!
I'm using WordPress 3.1.2 running as a multisite