setFeatureCompatibilityVersion issues a collMod to admin.system.roles. The AuthorizationManager receives a notification of this event, but is unable to understand what it means for the semantics of the collection. This results in the following error message:

2017-07-27T18:18:35.908-0400 E ACCESS   [conn1] Unsupported modification to roles collection in oplog; restart this process to reenable user-defined roles; OplogOperationUnsupported: Unsupported oplog operation; Oplog entry: { op: "c", ns: "admin.$cmd", o: { collMod: "system.roles" } }

After this point, privileges provided by custom roles no longer propagate to users.