[Madic]

Normaly I download the zip archiv and not the installer and extract MKVToolnix to c:\Tools\Portable\PortableApps\MKVToolNixPortable\App\mkvtoolnix\.

For testing purposes I downloaded the installer and installed it to the above path and also to D:\Program Files\MKVToolNix.
Now I know why that didn't worked and helped me with a symbolink link from C:\Program Files\MKVToolNix to c:\Tools\Portable\PortableApps\MKVToolNixPortable\App\mkvtoolnix\