I have encountered this same problem in the database (ms access) I am using to play around with LLBLGen for the first time. I will try to attach the diagram to more easily understand the issue, but it is essentially the same:
I have a table with a natural primary key, but also with a surrogate key (autonumber, Indexed No Duplicates) that, for whatever reason ( for simplicity in this case), that is used for all relationships defined on related tables. This is certainly a valid design, and not all that unusual.
LLBLGen didn't pick up this relationship as I had expected, wheareas if I make this the primary key, it then picks it up.
If the column is defined as Indexed No Duplicates (actually, it must be defined as such to be involded in relationships), then I think LLBLGen should pick up this relation should it not??
Thanks
PS: I attached a jpg of the diagram....in the diagram, I am talking about table report_instance, whose primary key is report_code&report_period, but the surrogate key report_id is used to define relationships to all other subordinate tables.