You say this system is new - how new is that?
What you describe sounds a LOT like an older fan showing signs of wearing out. Typically this is what happens for an older fan. First symptom is that the fan starts making an odd noise when it first starts up from COLD, but that noise goes away after couple minutes. If you reboot it does not make noise. If you shut down until the system is VERY cool then start up, the noise is back temporarily. Over some months the period of noise lasts longer and longer, and you may notice the fan running slow during the noise. Eventually the noise never stops. The last stage is the fan completely stalls and does not run. As a fan ages the bearing sleeves wear out and their hole gets slightly larger so that the shaft "rattles" in the sleeve at start-up. BUT as it runs the bearing parts expand and shrink that excess clearance so it can run smoothly. Further normal wear just makes this all get worse. The only solution IF this is your problem is to replace the fan. This should NOT happen to a fan that is only 1 or 2 years old.