And good to have around for moods.
Dwarfus, I owe you an apology. In my original reply up yonder I was completely unhelpful. I just nitpicked instead of offering anything. That sucks and I regret it. I'm sorry.
As to the actual question, though … I
don't know. I haven't figured it out yet, and I've been reading the real answers with interest. I had the same problem you described at Bannerskies, only with rope reed and sliver dye instead. I always, always ran out of empty bags. However,
this little mod to the game is incredibly helpful. It makes the milling-wheat-to-flour-and-filling-bags problem go away by giving you custom reactions at the quern or millstone. You can order only that dye plants be milled to dye —
specific dye plants, at that. Your millers will mill just what your order, and leave your cave wheat alone.
Now, there's a school of thought that says making a change like this to the game to get around a built-in mechanic is cheating. I don't think so, though. I think it's just an oversight. If you look at the jeweler's workshop, you can order specific gems to be cut, and used to encrust specific things. This is the same idea, only applied to a workshop that doesn't, by default, have those kinds of specific orders built in. Why should jewelers be able to take specific orders while millers can't? I don't have a good in-game reason. So I don't see it as cheating. In my game I even went so far as to add a bunch of similar custom reactions to the brewery, one for each type of booze in the game, because I sometimes like to micromanage what my dwarves are drinking. If I could figure out how to add custom reactions to the crafter's workshop to order my metalcrafters to stud only specific objects with metals rather than whatever happens to be near the forge, I'd do that too.
So while I don't have an answer for your, cause I have the same problem, maybe those custom reactions will help you find your own answer in your next game. (You can't add them to an existing game; adding new reactions requires a new world be generated.)