MacPro Hard Drive 3 TB or Larger formatted to Logical Volume Group by Disk Utility
This problem has been reported to occur on Intel MacPro's using internal drives from various manufactures with capacities &gt;= 3 TB. Specifically, it's been reported when using Disk Utility in OS X Mountain Lion (10.8) and Mavericks (10.9).
Although there have been solutions involving using diskutil in Terminal posted here at AskDifferent and elsewhere on the web, I found a simpler solution: Format the disk using Disk Utility from an OS X Snow Leopard (10.6) Install DVD.

Warning: This solution will cause you to lose all data on the drive.

Backup any valuable data from the drive in question.
Reboot using the OS X Snow Leopard (10.6) Install DVD. (Hold down the C-Key to boot from the DVD.)
Choose your language (eg. English).
Instead of installing OS X, choose Disk Utility from the Utilities menu.
Select your drive from the pane on the left of the Disk Utility screen.
Choose the Partition tab.
Select your desired Partition Layout.
Select Mac OS Extended (Journaled) under Format:
Check the Options button and verify that GUID is selected as the partition scheme.
Click the Apply button and verify you want to proceed.
When the partition and format process is complete, quit Disk Utility and reboot.


The disk will now be correctly formatted using a GUID partition table.
(If you need to repartition or reformat the drive in the future, you will need to repeat this process. Hopefully Apple will fix this bug in a later version of Disk Utility.)