Could be that I remember wrong and it's controlled by what's on the circuit (so the only farm that actually needs seeds is cocoa-farm -> only cocoa beans are allowed in there).
In case of pumpkins and orchard: They both don't need new seeds (since they're manual farms and you have to plant them yourself) that's why you cannot put them in there I think. Shouldn't be a problem, since pumpkins you only plant once and the agricraft-crops never loose their seeds either.
That's the reason I'm a bit unsure about the mechanic, used the farm too often with agricraft lately. But I guess in this case it's really just waiting till the cocoa-beans filled the seed-storage, then it should start putting any new ones in the output-slot.
Alright, thanks. I guess I'll just wait patiently.