To my eyes (and I do cosmetic repairs on bicycles for a living), it's rust. How and why? Hmmm, that's a tough one. If polishing doesn't do anything to change it (try a light polishing compound for automobiles and work it lightly into the finish), then you've got moisture trapped under the clear coat, which is causing the rust (or had caused, it might be done by now). I've worked on a few Masters, and I will say that sometimes the prep on these Colnagos isn't all that great, and they would go a little thin on the primer. That means that your paint will be susceptible to rust faster than normal. I'd bet that there is a pinhole in the clear and some moisture got in at some point. That area could easily have suffered a tiny chip from a stone or pebble being thrown by the tire.

You could try to find some color that matches, but I would highly doubt you'd find anything close. Plus, a lemon yellow like that wouldn't have the best cover strength, forcing you to do coat after coat of touch up until you've got a big blob on there