You should also report this to the game developer to see if they have any ideas.
After experimentation, the "loss" of my settings appear to be a Gnome3 bug. Using XFCE4, KDE, and even OpenBox standalone works perfectly fine. The game still doesn't recognize my primary monitor and provides no configuration to change it otherwise but at least I know what DM to not use (just started using it for a couple of days and already run into dozens of issues with graphics and interface configuration).
EDIT: For clarification, my settings will only be "lost" if I use gnome 3, otherwise the settings are restored after exiting the game just fine.
Nothing extracted yet.
When I first started the game, the game default to windowed mode on my primary monitor. When I went fullscreen and up'd the graphics a bit, it now /removes my current Xorg settings/. For example, my ViewPortOut and ViewPortIn setting is clearly set to default, my primary monitor is no longer available, and my secondary monitor is made my primary.
These settings persist until I restart X or reapply the settings via nvidia-settings tool.
If anyone would look into this for me, that would be great.