The company which had installed the new (larger system) and reconfigured the duct work could not find/fix the problems. I had 4 companies come out and have them give me a description of the issues along with a quote. 3 of the companies simply wanted to change out the duct work.
The last one (Climate Magic) did a thorough inspection and diagnosed the issues. So we hired them and they did a phenomenal job! Have had no more issues and thus we have stayed with them for all of our service.