I found the problem. Listed here for future generations (or more likely my 
future self). The classes for each schema I have are defined in separate 
files. In each I was calling

Base = declarative_base(bind=me.engine)

I was also doing the same in the class I have that wraps the database 
connection. It seems like these Base classes were different enough not to 
be able to share objects subclassed from them. Ensuring all used one common 
Base fixed things.

Thanks for the help,
Demitri

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