Hmmm... I always order a special meal (vegetarian) on all meal flights unless I'm booking at the last minute, and, *as far as I know*, it hasn't affected my ability to upgrade. I usually fly CO, NW, and UA. My upgrade rate over the last year has been at least 90 percent, and I have gotten a handful of operational upgrades. If I get upgraded at the last minute and they only have a Y special meal, they'll either give me the Y special meal on an F tray or let me choose. This has happened on totally full flights, so it can't be an issue of spare meals either.

They don't always remember the special meal in the first place, but that's another matter.

-Adam