Safemode prompt issue

Its not often that I come across something which totally stumps me but this is one of those exceptions...

I had a machine brought in today which was running really slow and locking up frequently, after removing the spyware junk choking the system it proceeded to start up and shutdown without issues... appart from 1.

Whenever the machine starts up it reports an improper shutdown and displays boot options of the 3 flavours of safemode etc. The machine both boots and shutsdown cleanly but always reports an improper shutdown.

Any thoughts?

machine is running
Windows XP Pro SP1

I've ran a full diagnostic on the harddrive and turned up nothing.
I'm assuming something is flagging the drive but im hitting a deadend here as to what.

Any suggestions welcome