I vote for a bat in the air ducts. Anything else would sound like running feet. We had a squirrel get into ours once from the old kitchen stove chimney which wasn't blocked up properly. Solution was to remove a section of duct, and leave a window totally open to the outside as the squirrel could smell the fresh air and be drawn to it. It worked.
Only other thing I could think of is something light has been drawn into the ducts and is blowing around in there. Good luck.