Cultures run from sputum samples are not at all conclusive. That, to me, is one of the most frustrating things about this disease. It's completely possible that your samples are coming from airways that do not have any infection present, while the infection causing your fevers is trapped in another lobe, another airway, etc.
Bronchoscopies are a bit better, but again, it is impossible for the doctor to see every little passage in your lungs, and even harder to TEST every bit.
One question that might be worth asking is whether or not your clinic routinely tests for mycobacterial infections. If they are an accredited center they should, but it still wouldn't hurt to ask. These tests take longer to grow out and pick up bugs like mycobacterium abcessus and MAC (mycobacterium avium complex) that can cause fever.
Good luck finding the cause of the fevers, and I hope you feel better soon!