Yeah, it's placement
Beroc's tool added a badge layer (the _badge.tga file) to determine where the badge went. If you extracted a banner with Beroc's tool, it treated it as an odd shaped banner and so gave you an _badge.tga image (even though it was extracted from the banner layer).
The Texture Tool will correctly add a badge position to the badge layer (from the _badge.tga) and a banner position to the banner layer (from the _banner.tga)
So if you want to make a new Crusade banner with extra details on it, you can - just make sure that the banner area is the right size and that you didn't extract it with Beroc's tool (because it will have saved it as a badge layer, which the texture tool will then reject by going "badge? you call that a badge? it's not square or the right size, you fool!" - only slightly kinder
)
As an update - there isn't a version released yet, but RSH extraction is now working
Just got to figure out how to put them back
[edit] RTX extraction and compilation is now working (used in Winter Assault campaign team colouring). The only step left is RSH compilation