Just to check, do you have room in the box for all the seeds you're trying to deposit?
I think the seedbox can only hold a few different types of seeds, so the way the logic works is that any time it gets a new seed it tries to fill the box. If the seed doesn't go in the box, the bot assumes that seed cannot be put in and stops trying for that seed type
Or if it's working correctly that's the logic
So my box is full with 6 seed types. It has Ranarr, Irit, Avantoe, Kwuarm, Toadflax, and Snapdragon in it.
I also have Cadantine, Lantadyme, Dwarf Weed, and Torstol stack in inventory.
The seeds I have noticed it fail to put into the box are Avantoe and Irit so far. But when I posted earlier and said it was working, I watched it click the Fill option on the Seed Box and put an Avantoe seed into the box. But around 2-3 hour mark, I noticed it stopped clicking on Fill and just left the seeds in the inventory.