Hi Headache6. I believe that it's from the TT and the fact that they don't have skimmers (?) in their cement holding ponds. I have a waterfall that is about 2.5 feet high and when I shut the valves to my two skimmers to feed the koi I do get lots of bubbles. Also, I notice that the bubbles are more prominent when I salt my pond. Besides, isn't this a good indication that the water is well aerated?
As far as medications I don't know if the Japanese breeders use any and if they do whether they are the cause of the bubbles.