Then you may be right and you are not supposed to change the material directly in the multisub-material. I don't know the plugin so I've no idea how it works. The script converts the materials recursively, it follows the material tree to the lowest branch and converts then back upwards until it reaches the multisub-material.
If there are specific material slots somewhere in the plugin it may be a good idea to drag those into empty material editor slots and convert them this way.
By the way, the multisub-material seems to have 999 material slots?! And all are empty (the first couple materials especially ID 1-20) ?
