Hey thanks for the feedback. The boxes puzzle may have been too much for the first puzzle. You can't jump directly onto the boxes they're too tall, you have to start from an elevated position. You have to jump onto the box from that first dark room where the box originally was. I'll post a video soon.
If your health drops too low you'll lose a leg.
As for losing the ability to jump? Off the top of my head I'm thinking the first ability, the power beam, locks you in place while you use it. (The beam is only used to power doors, bridges, etc, and I wanted to discourage players from trying to use it as a weapon.) I'm thinking if the power beam is active and the controller is receiving the jump command... I'll see if I can replicate the bug and patch it. That's for the feedback.
Hope you get to give it a second shot.