I've just tested a few maps (one with a rearm script, one without, etc) on a clean dedicated server with bots, and everyone spawned properly every time. If you have a specific thing people do that results in them spawning in weird places, then I can try to reproduce that, but right now there's nothing I can do.
edit:
Actually, I'll revert the specator changes (where they get parented to players they spectate). I think the first sighting of the issue was when they were first implemented, so it's worth a shot.
Grab SVN r640 and see if it helps.