It doesn't surprise me. My original pulmonologist told me years ago that 3 sputum samples, taken on 3 days should be submitted. This minimizes chance of contamination either by patient or lab. Also if the cultures grow different varieties, it lends credence to possible contamination.
He and my ID doc both used combined criteria for the decision whether to treat - bacterial load, CT scan and severity of symptoms. One must use a lab that measures bacterial load in the specimen as well as determining which Mycobacteria it is and antibiotic susceptibility.
There is so much to consider beyond antibiotic therapy. Controlling my asthma and doing airway clearance has been a lifesaver for me.

Thank you for sharing your Doc's comments. This is consistent with what I've suspected....hard for the docs to know for sure whether someone has an active infection, and how serious/extensive it may be, due to all the variables. The most frustrating part for me is having any sense of certainty if/when my infection is resolved and I can start the 12 months post conversion phase.