This was a strange one – I have a server with an external Thunderbolt RAID. Like most servers, I have permissions set on certain folders to limit access.
Whenever the RAID was unmounted and then remounted (or the server was restarted) the Ignore Permissions checkbox kept getting turned on again.
Fortunately there is an easy fix.
There is a text file in the /var/db folder that contains a record of the unique IDs of disks that have been plugged into the Mac, and whether or not they should ignore permissions.
Somehow, the Finder wasn’t updating this file properly when I unticked the checkbox, so the change would stay active until the disk was remounted, at which point it would check the volinfo database, and set the disk back to ignoring permissions.
There are two ways to fix this – quick and dirty, and properly.
The quick and dirty way to fix it is to just delete the file and let the system recreate it.
The proper way is to open it in a text editor and change the number after the unique ID for the drive in question. A value of 00000001 indicates that Ignore Ownership is turned off (i.e the drive will use proper file permissions) and 00000000 indicates that it is turned on.
You can get the unique ID of your drive in any one of a number of ways (Disk Utility, diskutil etc) and change the value in the file to suit.
In my case, there were five entries for the one drive, all with the same GUID, the first one had a value of 00000000, and the remaining four had 00000001. I’m guessing that when the file is read, it stops at the first match, which was zero. I deleted the additional entries and set the first entry back to 00000001, and all is well now.