Things are actually a little different.
The large flag means that the sprites of the character+weapon doesn't fit in the 64x64 size. In those cases the application fits the images in a 192x192 sprite.
This way the boomerang is a large weapon and the axe isn't.
This was me trying to not waste so much video memory. In the chargen I accomodate both sprites sizes by changing it's center position.
If this is not an option for you, you can try to change the parameter "export_large_sheets" to "always".
This will always export images sized like the boomerang ones, but at least it will be in a consistent size.
Hope this helped.