I don't think the "break-in" is on the moving parts (if any), break-in is used in this case as a term for building the bacteria up on the unit itself. Once the break-in is done (usually 1-2 weeks), the micro bubbles will go away. Additives in your water will also cause micro bubbles to appear. Give it some time, they should go away.
I know they are annoying, I had them too. They will go away.
125 Gal-35 Gal Wet/Dry-Tetra-Tec PF500 HOB
(3) AuquaClear 301 Powerheads-600 GPH
Automatic Tempature Controller
5-6 Inch Sand Bed-200+ lbs of LR