It looks like wxLauncher actually keeps its settings, including resolution, in its own location in the user's AppData folder; only when the game is launched does wxLauncher write anything to the registry. So, while wxLauncher is remembering its settings, it could still be failing to write the resolution to the registry.
Try running wxLauncher as an administrator. On Windows 7 at least, this can be done by right-clicking wxLauncher's shortcut and clicking "Run as administrator"; I don't know whether it's done differently on 8.1.
And just so I know, are you running 32-bit or 64-bit Windows?