I have been experiencing difficulties with some of the houses not upgrading from Tier 1 since the latest update. The houses affected are not storing any food, herbs etc and I guess this is the problem. They do store waste however, and this seems to be collected. I have tried to relocate the buildings, deleting them, rebuilding and flattening terrain - nothing works. Some of the houses has been this way for three in game years. The game was started on 0.7.5.
Your houses are probably full of guards/soldiers. They never come home so the home never upgrades.
I think there are other professions a bit like that too (maybe forager, hunter, etc…).