The system shutdown and sleep/hibernate/wakeup stuff is a known issue with some Linux 3.x kernels. This has been an ongoing work in progress. I think that some of the newest kernels have pretty much cleared this up, but I run Scientific Linux 6 (a Red Hat Enterprise Linux clone, much like CentOS) on my old Dell D630 laptop (a 2.6.32 kernel) and it has no problems with that stuff. It was a bug introduced in some of the 3.x kernels (major changes from 2.6.x). Do some Googling now that you have the system running well - you will find out what is what in that regard and can act accordingly.
BTW, have you tried shutting it down via the command line? IE, "sudo shutdown -h now", or "reboot" and then hitting the power button when it gets to the BIOS/POST?