Also noted in Darkhax-Minecraft/BotanyPots#353.

It appears that the bookshelf:load_conditions type bookshelf:item_exists is not detecting immersiveengineering:seed. Can't help any more than providing the following theory. Immersive Engineering recently switched to NeoForge, so maybe NeoForge items aren't registering (?). I could very well be wrong though. Happy to create an issue on the IE git as well, but if this is occurs for other NeoForge mods, then it might not be something they can fix.

False alarm folks. Turns out it was a different issue. My apologies. If you're experiencing the same issue, please follow the issue on the botany pots github linked above.