I've been made aware of an incompatibility with the GoG release and attached a fixed version of the launcher to the original post. Or just
click here (if you're logged into the forum). If you have the GoG version, you need to run the launcher as administrator to make it work.
For the technical minded:The GoG version by default launches with administrator privileges. In Windows Vista and above this causes the game to store its settings in a different part of the Windows registry than it would otherwise. To be precise, the GoG version stores everything in (in a 64-bit Windows version):
HKEY_LOCAL_MACHINE\Software\Wow6432Node\Mithis\Nexus - The Jupiter Incident
... while the normal location if not run as administrator would be:
HKEY_CURRENT_USER\Software\Classes\VirtualStore\Machine\Software\Wow6432Node\Mithis\Nexus - The Jupiter Incident
So basically, the launcher would look at the wrong key in the registry and thus not find the Nexus installation. I've made a few changes to how it discovers the correct registry key and it should now work with the GoG version out of the box. You need to run it as administrator, though, just like the actual game.