When changing the overlay map opacity the setting only stays for the zone you are in. As soon as you move to a new zone it resets back to 50% opacity. I have tried making changes from the login screen, after login, and after choosing a character. The setting only lasts for the current zone (if you are in-game) and then resets. If you make changes on the login screen, for example, as soon as you close the settings window it resets.
You can test this by clicking the settings button, changing the overlay map opacity all the way right and the overlay map zoom all the way left, and then closing the settings window. Click settings again and the overlay map zoom setting will still be all the way left, but overlay map opacity is now right in the middle instead of all the way right.