Yes, they may well polish out, but the whole point of having this done was to try to cut out some of the polishing. I'll certainly be mentioning the interest being shown by some on here to the outcome of this, if it has to come to that, but hopefully it won't and there'll be a solution.
Mike, I called round at Bill's this afternoon and he'd just got his back from the coaters. They were on the bench ready to fit. Probably not the best time to turn up and point out the brown dots in mine.
The more i look at it the more i wonder if perhaps the coating isn't fully cured untill it has a few hot and cold cycles and possibly you have ridden through something that had stained the finish before it had fully hardened it may polish out and never return
i would however take the bike to whoever did the job and ask them for advice or at least email them the photo's