So in this case it does seem that most likely issue of not being able to reference out by System is due to some issues in your Workspace configuration. As you have added some additional associated items for your components, you might need to create a static OPMS queries (stored in $(_USTN_PROJECTDATASET)ModelServer/).
Would you mind sending your current workspace for a review for me? You can upload it using the Secure File Upload: communities.bentley.com/.../7079.communities-secure-file-upload.aspx
It should be working fine if you use Unit for a reference, instead of a System. Can you please try that?
Regards,
Justinas