Windows won't start, can't login after first Spybot run

[john2718]

Last week my mother inadvertently installed SpywareBot. She
tried uninstalling it but couldn't get rid of it. Last night we
installed Spybot and ran it. It found about 60 threats including
SpywareBot. We asked Spybot to remove them and it said it was unable
to remove one threat because it was still running, and asked if
Spybot could run during the next restart. We said yes and
restarted the machine.

Now the machine won't start up. It gets to the login screen, but
after a second or two, before you can login, the system resets on
its own and restarts.

This is Windows Vista with Spybot 1.4.

I've tried starting in Safe Mode but that doesn't work either.
I just found out about Last Known Good Configuration and will try
that tonight. The only thing that has worked is one of the
Windows startup/recovery menus lets us open a DOS/command line
prompt.

Help! Is there anything we can hack or delete from the command
line to get the system to start? Anything else we can do short
of re-installing Windows? Any help would be very much
appreciated.

Thanks,
John

[john2718]

Booting into the last known good configuration worked so the system is back up and running. Spybot says everything is OK but SpywareBot still shows up in the list of programs. Is it better to try to remove SpywareBot by hand or let Spybot remove it? Any other suggestions, besides making a backup before we try anything else?

John