I'm running Structory 1.3.7 on a Paper 1.21.3#76 server. I also have Towers and several other datapacks and plugins, but I can reproduce this issue with only Structory on a brand-new singleplayer world as well so this doesn't seem to be an incompatibility issue.
On server startup, I see the following error in the console:
[16:38:10 ERROR]: Couldn't parse data file 'structory:harvest/old_manor/treasure' from 'structory:loot_table/harvest/old_manor/treasure.json': DataResult.Error['Item must not be minecraft:air; Item must not be minecraft:air': net.minecraft.world.level.storage.loot.LootTable@56f53fd4]