After testing in the Collector app again, we have now discovered it is the actual app that has the Username issue. I downloaded an area and went "offline", captured a couple of points and saved. Before I went back online I reviewed the captured data and the CREATED_USER and LAST_EDITED_USER fields were auto-populated with my managers name. I am definitely logged in under my name. This is quite concerning as we won't be able to track who captured the data for further reference! Is there a chance that when my manager created my login that I was created as an "alias" and therefore when I capture data it is saving as his username?
UPDATE - We discovered the CREATED_USER and LAST_EDITED_USER fields are being populated in the name of the "Owner" of the Feature layer, not the person who captured the data. Again this is not going to work for us as the person who owns the data is not going to be the one capturing the data. We may have over 20 people capturing data in the field but we can't track this work as it always populates with the GIS person sitting in the office.
We login to Collector with our ArcGIS Online credentials and then when we open a map we have to login again with our Server credentials (not ideal). My understanding is that when your Server is on-premise it is the Server credentials that are used for Collector edit tracking, not your ArcGIS Online credentials. I guess you can setup an on-premise layer with one set of stored credentials that are used by all users, or you can not store any credentials and then users will need to login to Server individually.
My manager and I have found that the problem doesn't actually lie with populating the current user, but the fact that when the features sync to the sde, then the "Initial visit by" ('CREATED_USER' field) and "Last updated by" ('LAST_EDITED_USER' field) attribute fields get filled in as my manager's username, not my username even though I collected the data and he didn't edit it. Any ideas on this problem?