Verify/repair permissions grayed out in disk utility

Select a drive then Press COMMAND-I to open the Get Info window. At the bottom in the Sharing and Ownership section pane look for a checkbox labeled, "Ignore permissions on this volume." It must be unchecked in order to repair permissions. If it's checked then click on the lock icon, authenticate, then uncheck that box. You may need to relaunch the Finder or restart the computer for the change to be recognized.

Repairing permissions is only meaningful on the boot drive. You can't do it to any other volume. Only you know what the permissions should be on those. If one of those other drives contains a bootable system, boot from that drive to repair its permissions.

Tom,

A slight mod. They are meaningless except on any volume containing a bootable system such as a clone or volume with another version of OS X.

Don't you have to boot from the disk to repair its permissions, though? Maybe I'm mistaken about that.

Tom,

No, you're correct if you want to correctly repair them on your startup volume. But DU will repair permissions on any selected volume that has a bootable system installed on it or a volume on which the, "Ignore permissions ...." option is checked. Of course there aren't any permissions on a data volume for DU to repair so the process goes really fast.

Okay, thanks for the clarification!

No problem. It puzzled me for a while. Now I check it every time I format a drive since DU doesn't correctly set the permissions needed. It's a pain that when you clone one startup drive to another, say for backup, and erase the destination in advance that the drive's ownership and permissions will be wrong. Then you try repairing permissions like the OP did and find those options are grayed out, and you are staring at the monitor trying to figure out why. PITA.

I installed a 2nd drive on my Mac Pro:
Disk Description : WDC WD1001FALS-00J7B0 Media Total Capacity : 931.5 GB (1,000,204,886,016 Bytes)
Connection Bus : Serial ATA 2 Write Status : Read/Write
Connection Type : Internal S.M.A.R.T. Status : Verified
Connection ID : "Bay 2"

There is no OS on this HD; but what if drive is acting slow? Should there be a way of checking &/or repairing?