Brett, did you figure this out?
I believe we are having the same problem (if I am reading your post correctly): I have published a feature service to ArcGIS Server that contains two feature classes and a GDB table that are all related to each other through two relationship classes I have created in our Enterprise GDB. These features all reside in separate datasets in SDE; one of the relationship classes was created in the same dataset as the source feature, the other was created outside the datasets in the general SDE directory.
I am having a hard time finding a best practices guideline on where to create these relationship classes and how that affects the permissions assigned to them when operating in SQL Server.
I was able to publish the service, and I can successfully switch between related features when using the service in a web app, but the service seems to run slow and I get a lot of generic "General Geodatabase Errors" in the logs.
Where should relationship classes be stored relative to their related features, and how do you check/update the permissions for them?
