I confirmed the permissions with my housemate. They're set right.
Any ideas? It seems like it has to do with those last two lines about child IDs in the fresh meat entity, but I don't really know what that means and I'd like to keep on keeping on and get through this.
I mean, it does seems like I can progress without making the tonic, but I really do want to "help" poor Agrippa. I might finish the game for what it's worth without this bit, but if there's a solution, it would be nice to employ it. Thanks.
EDIT: So I progressed, and as it turns out it looks like there is more than one well I can use to lower the meat. The glitched one is the one attached to the hallway leading into the Transept. The one found after being imprisoned worked just fine. It's still pretty baffling to me, but it looks like I can finish the game at least.....?