Newly upgraded TFS server has two user accounts created, "Project Collection Build Service" and "Project Collection Build Service (Team Foundation)". Both accounts have the same GUID (listed in the Username or Scope column). These were created by TFS and the GUID begins with "Build\" Attempts to delete either results in an error. Using TFSConfig to list user accounts, these do not show up.
To run builds, the Project Collection Build Service Accounts group must have, as a member, the Project Collection Build Service user account. Both of the accounts listed above can't be added to the group because of the matching GUIDs.
Every few hours, builds start failing with error stating
The workspace xxxx;Project Collection Build Service does not exist.
This means that the user account with the added (TEAM FOUNDATION) is in the group. If it is removed and the other one is added, builds start working again. Until a few hours later when the builds begin to fail with error stating
The workspace xxxx;Project Collection Build Service (TEAM FOUNDATION) does not exist.
Swap them again and builds start working. It appears it is applying the user account via the GUID but then doing some kind of verification based on the Display Name.
Some help pinpointing this error came from the post at http://www.codewrecks.com/blog/index.php/2016/01/15/troubleshoot-error-tf140 44-in-build-vnext-for-tfs2015/ but I can't find any other references to an issue with these accounts.