I have managed to reduce the bug to a tiuny test case. It seems that
this only happens when calling automodule directive on a package, with
code in __init__.py which registers a new GType. Moving the code to a a
regular module inside a package allows it to be imported normally.

I have attached the project directory, and there is a script "build.sh"
which just demonstrates how I run the builder to get the PYTHONPATH
correct to be able to improt the package.