well, sometimes someone is completely convinced he is right in an answer but then finds out he is wrong (and sometimes that someone is me), so it pays to have a second opinion
dwarfs take some time to get barrels and all the thing sorted out. It might have been the spawn issue, since the spawns are treated somewhat differently. You'll need bags for the plump helmet spawns. Only 2 bags to hold the maximum of 200, but if you have no free bags (the others are full with rock nut leaves, whatever they were called again?) they'll be stored on the stockpile, keeping it completely full and forcing your farmers to leave the grown crops to rot on your fields. After they were rotting away, they can take the seeds again, the stockpile will clean up, etc, until the next time it overflows with the spawns. That might not be what happened, but it's a good guess I think.
An important first step is to have enough bags, another important step is to seperate stockpiles. Having one seed stockpile, one for harvested plants, one for prepared meals and one for cookable/edible meat and fish, one for tallow (for soap instead of the oil, you always need lye anyway) and so on and so on. It helps overproduction or poor management to stop the rest of your works. Similarly, giving cloth and such their own stockpile just makes it easier to keep an overview of the running of your fort without having to scrutinize every stockpile closely or spending a lot of time in the stocks screen
for seed stockpiles: you need 2 bags and the space for it per crop you plan on growing, don't use barrels for it, that is more efficient