I have seen this a few times, maybe after some other error occurs that may seem unrelated. I just force a shutdown, then after a cleanboot, & following normal NAS/iSCSI operation, shutdowns seem to work again correctly.
Try and test with disabling the ACPI and or both the IO-APIC for some systems this seems to work.
Go to the Console and enter CTRL + ALT + T then select Boot Options then option 1 "Boot Parameters" there you will see the options to disable these features.