how old is he? I think it is probably fear based. Fight or Flight. He can;t get away and being forced to do something he doesn't want to do. He has no control he is being forced and is afraid.

Have you tried to get him to go up with treats and praise? You should make your leaving as pleasant as possible. His crate should be a safe place not a place to go that has started bad (being forced). He will associate the crate with something bad if he is being forced. By using trerat and a huge amount of praise. he will soon feel going to his crate when you leave has a HUGE payoff...he get treats and loving. after a while you can stop the treats and just use praise.