Sounds a little like separation anxiety. The problem isn't that he doesn't like the crate. In fact, it sounds like he's a-okay with it. The issue is that he fears being alone. In that case, try alone training with him. Here's an article, since I'm feeling too lazy to type it out:
http://www.wagntrain.com/SeparationAnx.htm

Pay particular attention to the "Short Absences" (scroll to the bottom). This is the most important part of alone training - training your dog, in little increments, to tolerate being alone.