I finally solved the user-created Schema problem last night. The issue was that the MainBody field in LearnerUI was created, but not initialised until the actual simulation was started (as opposed to the main GUI). This explains why Schemas with no States worked, and why it was possible to edit Schemas while the simulation was running.
I changed the LearnerUI class to initialise the MainBody immediately, and also changed MainBody so that the initial Schemas are not added until the start of the simulation.
It's a little annoying that the problem was so simple, but it's working now anyway.
The code is (mostly) commented and a few tweaks to the "One Step" feature should be all that needs to be done.
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