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[PatrikLundell]

I started my fortress using the Crimson Crops mod (increases growth time, reduces yield, season dependence moved topside, domesticated animal production rate reduced), but gave it up after a couple of decades as half of the surface crops didn't work. 10 years or so down the line I suddenly ran out of pig tail and cave wheat seeds. OK, I harvested some wild ones and got me a seed supply, but one year later, I am again out of seeds (with cave wheat, I have a single tile that has cave wheat for a single season each year, so they shouldn't even have been able to plant the seeds I collected). This discovery was done late autumn, beyond the planting season for both pig tails and cave wheat. I again collected pig tails and cave wheat, brew and threshed them respectively, and verified I did have seeds (9 pig tail seeds, 10 or so cave wheat). Seed cooking is off (verified), and I also haven't done any cooking since. Come spring I check my seed stocks, and I don't have any seeds of either of those crops! I've increased the total seed cap from 3000 to 10000 to ensure I can have the maximum number of seeds of each crop I plant (each is planted on a single tile for a single season, with the exception of plant fiber producing ones), and the number of seeds is 3400+, so that should be fine, and the cap culls production of new seeds, as far as I know, not destruction of existing ones.

Any idea of whats going on?

I've had similar problems earlier (0.40.24) without any mod, where I've brought garden vegetables on embark to get seeds, and end up not having the vegetables, nor some of the kinds of seeds before I start using the kitchen for the first time. On the next embark I didn't have the problem, though... I believe others have had similar problems.

[achamalacha]

This happens to me some times as well. Mostly because of processing seeds in workshops or the kitchen.

AFAIK if seeds are stored loosly in a pile, the get eaten by vermin. Storing them in bags reduces the risk of seed being eaten by vermin. An it is even better to store those bags in barrels

[steel jackal]

there is a cap of 200 seeds per seed type and a cap of 1000 seeds for the entire fortress

if either is exceeded seeds will be deleted

if you have a dwarf with plant gathering enabled and you have a plant gathering zone set to active then your dwarves might be creating more seeds than the 1000 seed cap, and thus your oldest seeds are deleted

[Quietust]

there is a cap of 200 seeds per seed type and a cap of 1000 seeds for the entire fortress

The default fortress-wide seed cap is 3000, not 1000. As already noted, you can increase the cap (or possibly set it to 0 to turn it off).

[Dozebôm Lolumzalìs]

I personally set the fortress seed cap ridiculously high. There's a bug that occurs when the individual seed caps and the fortress-wide seed cap interact; it gets rid of seeds, even when they were produced recently.

[PatrikLundell]

Vermin eating lose seeds could possibly explain it, although my cats are ranging over both the farmer's workshop, the still, and the underground seed stockpile, and the vermin is selective as well. Now, I have a huge number of bags due to my glass industry being reliant on import, so if the seeds are not stored in bags it's because the dorfs are lazy, especially at the emergency seed replacement productions, since those occurred during the R&R period where only the most basic activities were performed, and most dorfs thus were free from ordered labor. Early on, however, there tends to be both a dearth of bags and massive amounts of job category starvation due to all the jobs generated (Strip the surface of plants, cut down all trees, haul the wagon contents indoors, ...).

[Blue_Dwarf]

Dwarves sometimes take seeds to feed their pets. If you have a lot of pets, that could explain it.

[PatrikLundell]

I don't have a lot of pets. Maybe half a dozen cats, so they'd have to be rather selective when raiding the seed stores to deplete two kinds. However, I didn't know seeds were misappropriated like that, so it's useful info.

Edit: It looks like I'm blaming my dorfs for my own failure. I'd accidentally set the underground seed stockpile to take from links only. Hopefully fixing that will cause things to go back to normal.

[Blue_Dwarf]

I may be wrong about feeding pets with seeds as well, it could have been just plants.

[PatrikLundell]

OK, I believe I've found what caused the disappearance: Removal of Crimson Crops. It seems setting plots to fallow all year round did NOT remove the modded planting of crops out of season, so seeds were put down into the earth only to vanish. Tearing up the plots and rebuilding them stopped that.