Sometimes (this was on 7057 but not on 7048 -- I've for several reasons gone back to 7048) I noticed a long shutdown when I had an external USB disk connected --may have been pending I/O etc.
Check also there isn't a load of Networking activity taking place as well -- if you can physically see your router see if any of the lights on it are blinking madly and check the log --hopefully you haven't got an unofficial program like Photoshop CS4 from a torrent which is attempting to "Phone Back Home" for a license check etc.
Other things could be loads of system services / data bases (MySQL, SQL server etc) trying to shut down or paging files being purged etc etc.
Cheers
jimbo