After a lot of testing I have worked out that it is to do with the fact we have multiple relationships to the same feature class (issues).
E.g. Site to Signs, Signs to Issues populates the foreign key correctly
Site to Signs, Signs to Issues AND
Site to Bridges, Bridges to Issues does not populate the foreign key field in offline mode in for issues recorded against either the Bridges or Signs feature class.
This has been working for the last few months and the check system is about to go live so something has changed. Can anyone replicate this?
Thank you