I'm in the bottom of the guard tower in the room with two locked doors and several crates. I see the hole in the air duct above but I cannot jump into it to save my life. I've tried moving the crates. I've tried jumping off the single crates. I've tried jumping off the double crates. I've tried using my whip. And nothing works.
I haven't heard of that being a problem before. You should be able to stand on the crate and jump to grab the edge. Have you installed the patch for the game? (from www.lucasarts.com)
You should be able to get up there if you make sure that you are lined up properly. Stand back a bit and look up to make sure you are in the right place. Then step into place and it should work.
By the door where you killed the guard there is a crate stacked on top of another. Climb up that, line yourself up, and jump into the ventilation system.