No kidding. Haha, that helps me out a lot. I've been going back and forth with the Server admin tweaking stuff to figure out why all our queries seem to cap out at 1000. For crying out loud.
We were able to work around this by tweaking our queries to look like
ID IN (1, 2, ..., 999) OR ID IN (1000, 1001, ..., n)
It worked in my case.