I don't think the Ableton MIDI preferences matter since the plugin communicates directly with the hardware (For me it's working even with track, sync and remote all turned off, but I usually have track and remote turned on anyway)
Make sure you're running the latest versions of the RMX software (at the time of posting - firmware v2.0.1, remixbox v2.0.0 and VST v2.0.0).
Drop the plugin on a track, click settings and make sure "Plug&Play" is set to "ON". The "connect" icon in the top right should illuminate blue - you might have to turn the RMX-1000 off and on again to get it to connect.
Then for the hardware controls to work click the "link" button in the top left so that it is lit up in blue and saying "Link On".
Hope this helps!