While rebuilding sysusages and sysdatabases, disk refit may attempt to insert rows with duplicate keys because it finds duplicate data in two different devices.
Symptom: disk refit aborts with a message about an attempt to insert a duplicate key into sysusages or sysdatabases. disk refit aborts silently, without reporting the database or sysusages entry that caused the problem. This is the only form of the problem that causes disk refit to fail.
Corrective Action: Determine which device caused the problem, delete that device entry from sysdevices, and re-try disk refit.
tempdb is a common source of this problem, so if tempdb was previously moved off the master device onto a separate device, begin by dropping the new tempdb device to see if that fixes the problem.
You do not need to shut down and restart the server when correcting this problem.
To check for the other problems described below after correcting this problem, restart the server using -m and trace flag 3608 as you did initially for disk reinit and disk refit.