NTFS Permissions not behaving as expected

I have several hundred folders in a directory where somehow, the permissions have become all messed up. When I'm trying to take ownership with my domain admin account, I tick the box which says Replace owner on subcontainers and objects but the resulting changes do not apply to many of the sub-folders. I also want to use the Replace all child object permission entries with inheritable permission entries from this object.
I then have to go to each one (and there are quite literally hundreds) and set the owner on each one. This is a daunting task and there must be some way of achieving this en-masse. Currently I'm having to click the Continue button for hundreds of failed 'take ownership' attempts.
I've looked at the ICACLS and takeown commands but I can't figure out what I can use to force ownership onto folders although I have been able to bypass prematurely wearing out my mouse button with the /C switch.
Can anyone help please?

Thanks in advance.