Keep in mind that JK's physics engine is very primitive. Things like the player, thermal detonators or throwable crates have the "move=physics" entry in the template. Crates and such are usually based on _walkstruct or similar templates, which are "move=frame". If you want crates to move, you'd have to script them with a COG and move them between frames. This is how they were done in the LEC levels and is the best way to do it.
You COULD make your crates' templates use move=physics, but that presents two problems:
1. JK uses spheres for collision on physics objects. This means that, in order to have the crates actually touch the ground, you need to have their size and movesize be the radius (maybe diameter?) of a sphere that circumscribes the cube. This isn't too hard and really just a matter of trial and error. But since it's a sphere and you're using crates, objects will be able to move through the edges where the sphere doesn't cover.
2. You can't stand on top of physics objects.
If these are just decorative crates in the distance that the player doesn't interact with, you may be able to make them move=physics and they'll move automatically. If they interact with the player you'll want to move them with frames. Take a look at the LEC cogs for details on this.
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