I discovered a problem with the CRM update.
After looking through the code under /data
I can see that the system is capable of either figuring out the metadata dynamically (I think this is needed for the aggregate subpanels) or via a file.
There are a bunch of metadata files that define the relationships for the aggregate subpanels (like activities)
These files are within the custom/metadata folder.
Look for files named tasks_activities_1_<FIELDNAME>MetaData.php
These need to be removed as they cause chaos when the relationships are being constructed.