Are you launching Maelstrom.exe or Config.exe? That message should only appear if Config.exe does not understand the current, working directory. But if you are launching Maelstrom and you see that, I might have an idea about the reason. Open the start.ini file with a text editor like notepad and make sure the firstlaunch setting is zero. Do a search in the file to find firstlaunch and it should be this:
firstlaunch = 0
If it is equal 1, then Maelstrom.exe will launch Config.exe instead of the game and maybe that is why it can't find the correct directories.