I'm trying to start up a glass furnace, as I'm want to do, and I'm running into the same difficulty I always have when trying to maintain a robust glass industry or process quarry bushes. I have no useable bags.
Oh, I've got lots of bags per se, but every last one of them and every new one I make is sucked into the bag devouring maw of my seed stockpile. It's just a tile, marked to hold one barrel and nothing but seeds, and in that barrel is every bag I own, each holding one unit of plump helmet spawn.
And I know it's not dumb pathfinding either. Sometimes, I can wring some bags loose and I'll see them wind up in the furniture warehouse. It's on the other side of the fortress. The seed tile is in the middle of the farm/kitchen area. But when I brew some plants, I'll see another line of dwarves, each carrying one seed, going all the way across the fort to the empty bags, putting that one seed in, pausing, then carting the bag back to the farms.
Eventually I resort to dumping the seeds and filling them with sand, but every once in while the process goes back to normal and I have to do it again. And I don't like having to exploit the game's logic to make my dwarves do something perfectly sensible, which they know and I know (and they know I know they know) they're quite capable of doing. (Yeah, the seed stockpile is kind of an exploit, but it's a much more realistic one.)
In summation, my suggestion is that dwarves storing seeds always look for a bag already holding type-appropriate seeds that isn't full, before looking for an new empty bag to put seeds in.