if this is a Windows 7 system, try running the affected programs as an administrator. I'm guess that the read-only flags are set for non-admin users, so it's not saving your settings to the disk.
Just to add to this: Windows 7 doesn't treat "admin" user accounts the same as the main administrator account. In fact, by default, that account is hidden. What this means is that for a number of things - especially in protected folders such Program Files - you need an administrator override to write to the disk.
Your problem may be very different, but what I suggest if you want to determine if it's simply a matter of admin privileges (whereby for some read/write issues it ends up being impossible to get around because it wants an administrator password - a conundrum indeed since by default none is set and yet it won't accept a blank box!), is to exit to the elevated dos prompt (type "cmd" into the box in the start menu, right click the .exe that is searches and finds, and "run as administrator"). Then type "net user administrator /active:yes" and press enter. When you log out of your current account you will be able to log in under the now-visible Administrator account.
Log in and go to the security tab under the properties for your hard drive. Change it from read only and see if it holds the change when you close the properties box and log out then into your regular account.
If the issue is simply a matter of WoW being installed in your Program Files folder, I would recommend grabbing the whole thing and shifting it to the base of the HDD (C:\) or a games folder that isn't secured to be read only.
Oh, and to change it back so that the real Administrator account is hidden again, do the same but type "net user administrator /active:no"