I've got an issue where three identical seed types are not stacking - and they share all of the same stats in the same sequence, and each has only one NBT tag (sharing via /kubejs hand command)

This is on
Minecraft 1.16.5
Forge 36.2.4
AgriCraft 3.0.5 Hotfix

1 seed:
Item.of('agricraft:agri_seed', '{agri_genome:[{agri_gene:"agri_species",agri_dominant:{agri_plant:"vanilla:potato_plant"},agri_recessive:{agri_plant:"vanilla:potato_plant"}},{agri_gene:"chicken",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"cow",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"fertility",agri_dominant:{fertility:1},agri_recessive:{fertility:1}},{agri_gene:"gain",agri_dominant:{gain:1},agri_recessive:{gain:1}},{agri_gene:"growth",agri_dominant:{growth:1},agri_recessive:{growth:1}},{agri_gene:"mutativity",agri_dominant:{mutativity:1},agri_recessive:{mutativity:1}},{agri_gene:"panda",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"pig",agri_dominant:{agri_key:1b},agri_recessive:{agri_key:1b}},{agri_gene:"rabbit",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"resistance",agri_dominant:{resistance:1},agri_recessive:{resistance:1}},{agri_gene:"sheep",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"strength",agri_dominant:{strength:1},agri_recessive:{strength:1}},{agri_gene:"turtle",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}}]}')

2 seed:
Item.of('agricraft:agri_seed', 2, '{agri_genome:[{agri_gene:"agri_species",agri_dominant:{agri_plant:"vanilla:potato_plant"},agri_recessive:{agri_plant:"vanilla:potato_plant"}},{agri_gene:"chicken",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"cow",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"fertility",agri_dominant:{fertility:1},agri_recessive:{fertility:1}},{agri_gene:"gain",agri_dominant:{gain:1},agri_recessive:{gain:1}},{agri_gene:"growth",agri_dominant:{growth:1},agri_recessive:{growth:1}},{agri_gene:"mutativity",agri_dominant:{mutativity:1},agri_recessive:{mutativity:1}},{agri_gene:"panda",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"pig",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:1b}},{agri_gene:"rabbit",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"resistance",agri_dominant:{resistance:1},agri_recessive:{resistance:1}},{agri_gene:"sheep",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"strength",agri_dominant:{strength:1},agri_recessive:{strength:1}},{agri_gene:"turtle",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}}]}')

7 seed:
Item.of('agricraft:agri_seed', 7, '{agri_genome:[{agri_gene:"agri_species",agri_dominant:{agri_plant:"vanilla:potato_plant"},agri_recessive:{agri_plant:"vanilla:potato_plant"}},{agri_gene:"chicken",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"cow",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"fertility",agri_dominant:{fertility:1},agri_recessive:{fertility:1}},{agri_gene:"gain",agri_dominant:{gain:1},agri_recessive:{gain:1}},{agri_gene:"growth",agri_dominant:{growth:1},agri_recessive:{growth:1}},{agri_gene:"mutativity",agri_dominant:{mutativity:1},agri_recessive:{mutativity:1}},{agri_gene:"panda",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"pig",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"rabbit",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"resistance",agri_dominant:{resistance:1},agri_recessive:{resistance:1}},{agri_gene:"sheep",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}},{agri_gene:"strength",agri_dominant:{strength:1},agri_recessive:{strength:1}},{agri_gene:"turtle",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}}]}')

Any idea why they're not stacking?

This is due to hidden genes (stats). The stacks have different hidden genes values
In your case :

• 1 seed : {agri_gene:"pig",agri_dominant:{agri_key:1b},agri_recessive:{agri_key:1b}}
• 2 seeds : {agri_gene:"pig",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:1b}}
• 7 seeds : {agri_gene:"pig",agri_dominant:{agri_key:0b},agri_recessive:{agri_key:0b}

So they are not really identical, and thus are not stacking.