Quick question: Did you scold him or do anything that would cause him to negatively associate the crate when he had an accident?

Another quick question, are you *sure* he didn't have an accident on his new bedding? And did you clean his crate very thoroughly after his accident? I would double check, just to make sure that there's no urine/poo smells in his crate.

Also, here's a big red flag:
Quote Originally Posted by absolut1377 View Post
Almost everynight about 10-15 minutes after we put him in (and after he goes to the bathroom) he starts crying like you would expect a new puppy to do (he's 1 1/2). Typically if we go down once tell him to be quiet etc.. he is fine.
Quite frankly, he's got you guys trained well He has learned that, when he whines, he can expect you to go down and comfort him. Worse yet, he's put it on a schedule (about after 10-15 minutes), so now you're on his schedule!

Assuming that he is healthy enough to hold his bladder, I would start back on Square 1 with the crate training. Rather than treating the crate as a "dog-goes-in. dog-gets-locked-in" type of tool, treat the crate as a game of sorts. This way, your dog will form a very positive and favorable association with the crate. (By the way, Susan Garrett really captured the essence of this in her phenomenal DVD, "Crate Games", if you want further examples.) Basically, you click/treat your dog for any positive interest or interaction with the crate. Eventually, you "shape" it so that the dog voluntarily offers the behavior of going into the crate for the click. This process of offering behaviors exemplifies the central beauty of clicker training. When the dog begins offering to go in the crate by himself, the positive association is complete. Then, you start doing self-control/"wait" games to really solidify the dog's desire to be in the crate. If you're confused about any of this, just let me know, and I'll explain it more in-depth