Some roots and tubers have different short descs before and after being cooked. However, although the descs are different, the same keywords still work for the roasted ones after the change. Mottled reddish roots, for example, turn into roasted reddish roots when cooked. Yet the keyword 'mottled' still works for the cooked roots. If a person has several raw roots and one cooked one, using any of the keywords to try to cook one of the raw ones is thwarted and you get a message saying you can't craft anything from the cooked root. That means in order to continue cooking more of the same, a person either has to drop the cooked root somewhere, or put it into a container before continuing. Is there some way this can get fixed?
I've never noticed this problem, but if it does exist, does "craft 2.root" or such work? I'm not sure. Been awhile since I've been cooking and didn't run into the problem even cooking multiples of the some one...
Also, if you are having the problem. Pull them out one at a time. Get one out, cook it, pull out the next one. SHOULD put it on the top of the list.
Creeper
I tried it with the numbers, and in most instances it doesn't work.
D'oh, I forgot to log back in before posting that!
I have never had this problem, and I've had several characters who would cook roots in batches. So, either something's recently changed, or you're cooking a root I never came across, or your problem is in actuality something else.
I can't think of anything to suggest except what Creeper said: take them out one at a time.