I don't quite understand what you mean by 'change the focus' in the launcher. I personally never use the launcher so I'm not exactly sure how it works. The best way I've found to have multiple installations is to install the game once, then rename the Dangerous Waters folder (on the hard drive, not the start menu) and install the game again. This way you can swap out which version you play by simply renaming its folder 'Dangerous Waters' (or whatever the installation path points to). You probably have multiple versions installed seperately and it's likely there are some shared registry entries between them which could be causing the problems you indicated.
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