Boxers are known to have a high incidence of separation anxiety. I agree with Dr. Doug. I think your pup needs some medication to go along with your training.
Do you leave a stuffed Kong in the crate for him? I smear p-nut butter around the inside of a Kong and freeze it for our two dogs. It helps keep them occupied for the first 15-20 minutes right after we leave them in their crates. I now just say crate and show them their Kongs and they run for their crates. You might want to try this on a much shorter term basis at first. I also leave an elk or deer antler for our dogs to chew on in their crates.
Also, I'd feed your pup in his crate (put the bowl at the front at first, eventually moving it further and further back in the crate) with the door open (you're feeding 2x daily, right?), so he learns that good things can happen in a crate. I always do this with new dogs. Eventually, once the dog is eating totally inside the crate, push the door 1/2 shut, but don't latch it while he eats (if he pushes the door open, that's okay; try again the next meal), then after he's comfortable with this, push the door shut, but don't latch it. Eventually, latch the door (open immediately if he gets upset) - this might take quite awhile to get to this stage. Baby steps.