I have upgraded from 5.0 to 5.1 and scanned the WP installations with the lscache whm plugin, a lot of the paths are listed duplicated after scan...what could be the reason? i.e.:
It is strange that you are seeing duplicate entries. Would you be able to pm me server access so I can take a look as to why this might be happening for you?
The newest build of 5.1.7 is now available. Try force reinstalling it through WHM and then running another scan. Your duplicates should no longer show up in the list.