For anyone else having this problem, this is how I managed to get rid of the user. It looked like the user was still in the userconfig table.

* Export of the userconfig table:
c:\> bcp besmgmt..userconfig out c:\userconfig.txt -c -T

* Then see if the user exists in the table and look for the ID at the start of the line. Then type:

osql -E
use besmgmt
go
delete from userconfig where id=id

Hope this helps someone.