All of a sudden refuses to sleep in crate

Question
My golden pup is 3 1/2 months old.  We got him when he was 7 weeks old and have crated him at night since day one.  He was doing just fine until this week when he made 2 "messes" in it, and now he won't sleep in it at night.  He goes in like normal, lays down, but in about 45 minutes starts barking to be let out.  Normally this doesn't happen until morning when he REALLY needs to go out.  We have tried to let him bark until he figures out that we are ignoring him, but he will go on for 30 minutes or more. I'm not sure if he is associating his "messes" with his crate now and doesn't like it, or if he's just trying to train us into letting him out when he wants all of a sudden.  Any advice?

Answer
Usually the place to start when a behavior problem crops up is the vet's office.  You can't train a physical problem away.

Have you obedience trained him?  Up until dogs are mature at 3 years old, they keep deciding to challenge the leader.  The key to most behavior problems is approaching things using the dog's natural instincts.  Dogs see all the people and dogs in the household as a pack with each having their own rank in the pack and a top dog.  Life is much easier if the 2 legged pack members outrank the 4 legged ones.  You can learn to play the role of top dog by reading some books or going to a good obedience class. A good obedience class or book is about you being top dog, not about rewarding standard commands with a treat. Start at http://www.dogsbestfriend.com/  Try these gentle ways of letting him know you are top dog:

''Elevation for small puppies:  Sit on the floor and gently put your hands around your pup's middle, below his front legs, and lift him up.  He is facing you.  Hold him for 15 seconds.  Repeat until he no longer struggles.  If he is past 10-12 weeks, lift his front feet off the ground, but don't pick him up.  

Cradling for small puppies:  Hold your puppy gently on his back, as you would cradle a small baby.  If he struggles, hold him firmly until he quiets for 10-15 seconds.  With larger pups, you can do this as your sit on the floor, with your pup between your legs.

Quiet lying down:  Place your pup on the floor on his side, with all 4 legs pointing away from you.  Use your hands on his neck/shoulder area and middle, to hold him in this position.  When he is quiet, praise him.  Lengthen the time that you keep him quietly in this position.  When he accepts this position well, handle his paws and muzzle, while keeping him quiet.''

The quotes mean this isn't my original work.  It is copied from my Puppy Raising Manual.  I have long used these or minor variations of them, and they are very effective.  You may want to give him a belly rub while he is on his back too.  Helps bonding.  There is a big difference between him rolling over and demanding a belly rub, and you choosing a time to roll him over and rub his belly.  The latter cements your place as pack leader.