Update: Still working with ESRI - they are trying to replicate my environment, which is as follows;
Single virtual server (Win 2012 R2) hosting 10.4 versions of ArcGIS Server, Portal and the Data Store
Security setup is using the Enterprise Logins via SAML to talk to our ADFS server (v3.0)
I can create the referenced log entries with ArcGIS server Federated or not Federated - doesn't seem to matter; the services secured or not secured...but as you all have noticed, everything seems to work.
Collector app consuming these seemingly running fine feature services, however, seems to cause the services to eventually crash...they restart, though. Not sure if related...
I'm going to see if I can recreate this issue in a 10.3.1 environment...