I've been having a similar problem with my youngest puppy right now!
Well ok first of all, she isn't really my dog, she belongs to my roommate, my hubby and I went and got her and brought her home for him because seriously- the dude needed a dog. BUT he and my husband work a lot, travel far from home, gone regularly, not here more often than not, so she's in my care, and in my bed, and as much a part of our pack as the other two dogs.
Right now, the guys have been gone for a bit over a month and it hasn't been often that they've been gone that long since we got this puppy so it might have something to do with this....
She has been doing GREAT going outside for the last 3-4 months, the only accidents she's had in that time is right in front of the door and only if I haven't been making sure to let her out often enough. About two weeks ago, I started going CRAZY cleaning the house for an appraisal (that didn't happen and took an extra week in which time I was super-crazy about keeping the house clean) and since I started cleaning, this little puppy has been peeing on the floor. And popping a few times too. Upstairs in my daughter's room, not necessarily a place I spend a lot of time.
We've been talking for so long about getting gates so the dog's can't go upstairs but with the guys home for 3-5 days and gone to work again for two weeks (has been their typical schedule), they haven't yet done that and I'm pretty sure they want something more than those little wooden child saftey gates that my block-headed male, aptly named "DOZER" would just bull right into anyway, otherwise I would have gotten them already....
So thats me sharing a personal story, I can't say I have much advise but you're not alone and I too appreciate the helpful advise that others have given here!
I think I will definitely be getting some of that enzyme cleaner, I know that Natures Miracle IS a miracle because I used to keep their de-skunkafier on hand at all times and lemme tell you it works wonders!! Even that one time I got a skunk caught in one of my live traps and my entire yard stank and I put some in a spray bottle.... yah.
(I'll definitely continue to work with her on the behaviors too, its so hard to train puppies within a group of three dogs, much different than training ONE puppy at a time individually)