TRACket Paul,
Yes, yellow rust. Not a theory, but facts based on experience.
I had the sunroof leak on my wife's Saturn while it was under warranty. Saturn replaced what they called the "Drain Pan" assembly that surrounded the sunroof and said that it had rusted out and was leaking. They replaced the pan under warranty but said that they could not pay for any interior damage. Fortunately, I caught it early and it only made a very small stain on the headliner just at the very edge where the fabric stopped at the sunroof and when the sunroof was closed, you could not see the spot.
The car was black and had a light grey headliner but the stain was yellowish. If you opened the sunroof and looked at the edge of the headliner from the outside you could see a darker red rust stain, but when it bled throught to the inside it came out yellow. It may be that the fabric is filtering out the red rust color and only a faint orange stain stain is getting throught and it shows up as yellow. The color shift may depend upon the interior color??
Also, rust can have a lot of yellow color tones in it, and if you take a rusty piece of metal and brush it with a wire brush you will see the red color get much lighter and even turn more towards a yellow.
...Rich