You may have an issue with the carpet or rodents. I know this is not what you want to hear, but even though the apartment complex may have cleaned your carpets, that does not get into the pad. Any previous pets or rodents that inhabited your apartment will cause what you are talking about.
I would suggest that any time your pup goes in the apartment, clean it up with vinegar. This helps remove the odor and helps keep the pup from reusing that area.
If this doesn't help, I would suggest you talk to your vet about behavior problems and stress on your animal. Your pup may need something to take the edge off until you get into your new home.
I'm sorry you are having to deal with this, but as with children, it is an adjustment for your four legged babies too.
Good luck!!!!
Jodi