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I like box jumps for weightlifting. It's a very simple, accessible way to train explosiveness. What I don't like is when box jumps are done in ways that reduce their effectiveness or create problems.

The point of box jumps in the context of weightlifting training is to train knee and hip extension explosiveness—it has nothing to do with conditioning or lifting the feet really high (although quick hip flexion is useful with regard to moving under the bar).

To make sure it's actually the legs and hips doing the work, you can simply remove any arm swing. I like putting my hands together in front of my chest—not clasped, but loosely in case I have to save my face from punching the edge of the plyo box. You can jump higher with an arm swing—but an arm swing isn’t magically making your legs and hips more powerful, so it’s a false inflation.

I also prefer lower boxes. This seems odd, I know, but with excessively high boxes, I find people typically will put more effort into lifting and reaching the feet (with a ton of back rounding, making this hip flexion less transferable to the third pull of the snatch and clean) rather than actually jumping. With a slightly lower box, the athlete can focus on a maximal jump and then coming down softly onto the box without a concern for missing.
 
If the box creates problems for you, it’s really not a concern—get rid of it and do standing vertical jumps. This is the truest vertical jump motion since there’s no need to move forward onto a box, and you can still add hip flexion if you want—just do it with an actual squat motion with the trunk set tightly as you would when pulling under a lift.