I have a newer house that is about 5 Yrs old. The second floor is always a little cooler than the first floor in the winter and hotter in the summer. The master bedroom and bath are always colder or warmer than the rest of the second floor and even more than the first floor. I have tried to install a booster fan in one of the ducts but that just seemed to work in the summer. I've tried adjusting the dampers. I finally came to looking at the cold air returns. And I noticed that the master bedroom is connected to the cold air return on the first floor. Where all the other rooms have their own return back to the furnace. Would this cold air return for the master bedroom/bath have an affect how the master bed/bath are heated/cooled? Also, all the returns on the first floor are at floor level, where as the second they are at the ceiling.

A small thing that may help is if you have stamped face registers in you bedroom you may want to replace them with a better register. The proper register for a ceiling will have adjustable curved blades that can be adjusted to throw the air through out the room and they can be purchased in one way, two way, three way and four way throw depending on the location of the register. Good luck, Mike

It is a good possibility that the return is to small.
It is a possibility that the supply for up stairs is to small also.

The only way to know for sure is to do a manual D and find out what size the ducts are supposed to be.

Be thankful this is the only heat problem you have. Builders always cheat on the HVAC so they can spend the money on better kitchen cabinets so it impresses the wife. You cannot see HVAC duct unless you are in the basement and most people have no idea what all that shinney pipe does. LOL

The only cure is to find out the right size. Tear out the old and replace with new. This is why I stress to new home buyers to have a manual D done for duct work and a manual J done for equipment sizing. It is the ONLY way to be sure of a good HVAC system.