Just for anyone having the same issue, I’m posting how I fixed it.
Now, I’m by no means a PHP developer, my background is c#.net, but by looking at code in the plugin, I noticed that the line 244 in cmetric_sbcfw_setting_functions.php under includes re-sets the $new_match_zone_arr array everytime it iterates through shipping methods in the zone, therefore clearing the array everytime a shipping method is found under the zone.
I changed the line to use array_push instead of setting a new array every time the loops comes through, therefore returning all instances of the shipping method, instead of resetting the array everytime it hits the loop.