Pardon me if this sounds "off," but I'm still wondering if it might be oxidation. Here's why I say that: The first oxidized boat I went to buff out (back in the 1990's), I fired up a Home Depot type buffer, put on some heavy duty rubbing compound and went at it. No dice. The shiny, gleaming boat I had envisioned just wasn't happening, and I couldn't figure out why.
Then the guy whose boat shop I was parked at came by and asked how it was going, and I explained. He came back out with this huge/heavy/metal Milwaukee buffer, put some of the same rubbing compound on and went to town on it. Next thing you know that section of my boat was gleaming! So all I had to do was do that to the other 99.5% of it :lol:
The secret was in the buffer, and in buffing it a bit longer toward the "until dry" stage. But mostly the buffer. Thereafter (at least, when I could move my arms again), I would always rent the same type of buffer for a day or two when I wanted to buff a boat. Eventually, I bought my own Makita 9227, and that's what I use now (with good results). So, I was just wondering if it might be possible that your boat would buff out nicely with the right buffer/compound. How were you buffing and with what?
(Now of course it could be as you say, something besides oxidation -- and for all I know you are a professional and have buffed out 47 antique cars; but given my first experience I just thought I'd throw this out there.)
Edited to add: Oh, and if your spots are like little white dots or "milky way" rows of dots connected together, it may be that the original gelcoat was a bit too thin in certain areas (or had "pimples"), and has thus worn through to the white below. If so, then you'd have to re-gelcoat or paint to get color back.