Hello Lizanne,
I have investigated your issue and I believe the cause of this irregular behavement is corrupt data in the MxModelReflectionModule.
For instance, if you sync Module A with has microflows which return objects (entities) from Module B, but module B is not synced, ValueTypes (coming from the synced microflows) are created in the database which are not associated with MxObjectTypes (which are not available due to not syncing module B).
Unfortunately syncing the Module B afterwards does not result in the existing ValueTypes being updated.
A solution could be to delete the corrupt ValueTypes through an adminpage and syncing the modules again. That way the ValueTypes are created again and have a association with MxObjectType. Be sure to check your existing TemplateConfigurations for correctness after this.
Ps, unselecting all modules and refreshing does not solve the issue. In the MxModelReflection ValueTypes are only deleted when the MxObjectType is deleted. Unfortunately the corrupt ValueTypes still exist because they are not associated.
What happens when you remove the module, run the app and then add the module again and sync again?
If all values are then created it might be an issue in the module with updating existing values.