You are using an Ubuntu/Mint/Debian with an Nvidia driver (or perhaps another proprietary GPU driver), and your custom resolutions are lost at each restart even though you applied them and saved to xorg.conf. This frustrates you to no end, and even if you script a live modeline change putting your box to sleep or a reboot will mean it doesn't get automatically reapplied. Also, your settings don't get reloaded into the settings GUI after a reboot, and you are mystified.
The built-in Mint Preferences > Displays tool doesn't give a crap about your custom configuration, and it will reload whatever it had set previously just to torture you. You can kill it with fire though. To see if it has a settings file look for a ~/.config/monitors.xml file.
You may not need the first four steps, or you may have already performed them.
- sudo nvidia-xconfig # create a fresh xorg.conf
- gksudo nvidia-settings # set it up like you wanted it; my overscan fix example
- Click "apply"
- Click "save to x-config file"
- rm ~/.config/monitors.xml # get rid of the non-xorg Displays configuration
I have seen this problem again and again on forums where nobody knew that deleting that file would fix the problems. Spread the word my friends.