I have a very traditional normalised SQL Server database that uses a common Lookup (Reference table). Qlik Sense attempts to create Associations and is successful on the main tables, however it fails on the reference table and I need to force the association.
Rename (in the preceding load part of your script) the key fields (by using AS) to have exactly the same name.
Qlik has a pretty clear standard if it comes to association: If it has the same name, it is the same thing. If it does not have the same name, it is not the same thing.