I also have this behaviour - shutdown doesn't power off the machine, but reboot does reboot, although some times the BIOS splash screen seems to take ages and hang at that point - I haven't really checked thoroughly but when that happens I can ctrl-alt-delete and it will reboot properly. This is on a Sony Vaio VGN-S460. So I don't know if some BIOS thing is not being reset properly, causing it to hang/take forever?
I also have this behaviour - shutdown doesn't power off the machine, but reboot does reboot, although some times the BIOS splash screen seems to take ages and hang at that point - I haven't really checked thoroughly but when that happens I can ctrl-alt-delete and it will reboot properly. This is on a Sony Vaio VGN-S460. So I don't know if some BIOS thing is not being reset properly, causing it to hang/take forever?