No problem - it's one heck of a buzz to have people come back and say things are better and they have happier dogs. To me that is the bit that matters. The fact that people find they can enjoy their dogs even more after changing a few things is a bonus, taking the stress and worry out of doggy life is the ultimate reward.

There a couple of things you can do to see some improvement straight away but it will only work if you can perrsuade your roommate to do them too. It must be total commitment or you run the risk of sending out even more confusing messages to the dogs and the situation will deterioate further.
First off you MUST take pressure and stress away from Jack - he isn't coping with trying to be the leader and is panicking. He is scent marking (Yep poop too!!) when the pack is split. He feels like he has been elected leader by the pack and it is his job to protect and keep the other members together. He doesn't know how to cope when the pack he should be in control of splits up and leaves. To ease his stress he turns to making the den safe, secure and strong so that if the lost members come back they will be safer and less likely to get lost again. To a dog this means smelly messages! He simply can't help himself.
On top of this he has a young pretender to contend with and an owner that follows his instrunctions rather than directs him.
Things need to change for this poor boy - does he chew? Does he self mutilate or is he destructive at all? If not, then he is probably heading that way.

The two humans in the house must start to take control of the pack. Take the responsibility away from Jack and let him relax and just be a dog.

You must also, once you begin the process of destressing Jack, sort out the more dominant of the two dogs. If left to do it for themselves, especially with two pretty well matched animals, there will be trouble. If Jack is still marginally above Duncan then he needs support in that role. If he doesn't get it then Duncan will constantly challenge.

Have a chat with your roommate and if she agrees to give things a go - suggest trying it my way for three weeks - let me know and I'll give some things to get you going. Both dogs will benefit greatly and the whole atmosphere will change, I promise. But, you must both agree to stick to it.

Good luck!