Can you RE-introduce a crate or crate training to a 15 week old dog?

[Matthew K]

Our 15 week old Rottie pup does have separation anxiety, but it appears he also has an anxiety towards being in his crate. 10 minutes ago I decided to move the crate out of the bedroom and place it behind my office chair so he would be right in the room with me. He was in there MAYBE 5 minutes and peed...and laid in it. This is the norm. Of course he had been out prior - as always - and had been playing free here in the office for the last hour and a half. There is no urinary tract infection, as a sample has been tested. I have since learned that we didn't fully introduce the crate correctly early on, so I wondered if we could somehow re-introduce it correctly so that this problem will not exist? He holds his urine in there from 11p to 6:30a without fail EVERY NIGHT, but during the day when we are in and out or gone to work (and one of us ALWAYS comes by around lunch to let him out) he pees.

The crate is the right size, we have special "crate-only" toys or treats, he gets exercise, he gets attention. It's just not normal for a dog to pee and lay in it. I understand the separation anxiety will be something we work on with medication and with a behaviorist, but I'm hoping the kennel anxiety is something we can cure on our own. Any suggestions? And please, no comments about a crate being cruel. You don't know what you are talking about.
Oh yeah, and we do use an enzyme killing cleaner on the crate floor.