Hi,
Thanks for the report, the video is really helpful. That could probably be considered a bug - seems like ngSkinTools tries to compensate weights to a total of 1.0, so when you have influences "A" and "B" on the vertex, and remove weight on A, it adds to B; when you remove from B, it adds to A.
One way to solve this is to actually control layer transparency via mask alone. Try this:
* From the ngSkinTools menu, go "Edit" - "Convert transparency to mask"
* Adjust influence weights them via approach "let's only " - basically all weights for each vertex is 1.0