I did install the HIVE cleanup service to see what is going on.
There were some events regarding RTVscan.exe which would have been when SEP was loaded. (KHCU\Software\Symantec\Symantec Endpoint Protection\AV\Custom Tasks (0x808) was preventing the profile from being unloaded).
I removed these task manually using regedit, and the error still persisted.
I then removed SEP... so I don't think it is related to SEP.