I'd have to agree with Jojo. She had her puppies in your room so she now 'owns' that room, puppies gone or not. From my experience with a different breed, it's usually the girls who control and your b itch is no different. And for sure, re him not being good with other males, with the less than dominant sort, they tend to adopt an 'attack is the best form of defence' attitude - true alpha dogs don't need to. In general.
Get her spayed so she doesn't become pregnant again. To have two living under the same roof who are right for each other, physically and on paper, would be pretty rare. Had they both been scored (HD and ED)? We bought in our foundation b itch intending to breed her with one of our then 2 males. By the time she was the right age, I'd learnt a thing or two about my breed, and took her to another stud dog as I saw putting them together wasn't going to produce the puppies I'd hope for.