When I startup my computer and logon, command prompt appears with this text typed in:
shutdown -r -t 3 -c niglet

After that it shows a system shutdown message which says it will shutdown in a number of seconds and that just keeps counting down until zero.

I get round this usually, because I run loads of programs on logon and this stops it shutting down. A lot of bother though, so I would like it back to normal.

It may be a virus or spyware, but I have scanned with AVG Anti-Virus and AVG Anti-Spyware. Both of them found threats but all the threats found were removed.

Please read THIS and after completing the steps outlined post a HijackThis log over in that section along with a brief description of your problem.

Do not post HijackThis logs in this section please.

I have scanned with spybot S + D - All problems found were removed.
I have scanned with Ad-Aware - All problems found were removed.

The problem still remains so I am now going to post my hijackthis log which I created in the correct section. Thanks for all your help.