The log shows that the plugin is loading both Genius and Musixmatch sources twice--once from the ones built-in to the plugin and a second time from the external yml files, which could well be messing with your results. You should un-check the external yml sources if you want to use the internal ones for the same source.
The selection choices in MB are shown using the internal name of the yml (first line after "name: ") not the name of the file. This will be confusing if the names are the same for both internal and external sources (I see your Musixmatch yml is an example of this). Either be sure they have a unique name internally, or, if you are going just with the internal ones, remove the ymls from the Providers folder entirely and re-start MusicBee, then re-select the sources in Tags(2).