It's hard to say with processed foods. Like the PP said, you don't really know what is in the "natural flavours", sometimes that is a hidden name for MSG. I also looked at the ingredients and they list Oleoresin Paprika, which is an oil from Paprika used to colour food. I'm not sure if there is any "hotness" to it, or even minor enough for a baby to react to. If she gets the red cheeks every time I'd assume it is something in the Velveeta. The cheese sauce they use in the vegetable mix you made could have completely different ingredients. I'd definitely compare the two.
If she is fine with wheat, dairy, soy, then I would assume it is the additives that she is reacting to, and just avoid that food for awhile. Hope this helps