I can't find the object settings offhand in CM but isTransparent should also be true.
This one single tip completely saved me just now from pulling my hair out ;-)
I tried for days to fix the glass objects on a car and (thought) I tried every permutation of shader settings to make it happen but completely overlooked this one super important detail in KSeditor!
PS: for everyone wondering - I do believe this flag can sadly not be altered in CM (just as you cannot change the actual shader used directly in CM). You have to set this flag in KSeditor.
Here is the easiest way I am currently jumping back and fore between KSeditor and CM to make such shader changes:
1) initially set your correct shaders on all objects in KSeditor
2) export the KN5 file and open it in CM
3) make all shader changes as desired
4) "unpack KN5" in CM (this will create among others a fresh persistence file with all your shader edits in CM)
5) load FBX file with new CM created persistence file into KSeditor to make any more "deep" shader settings (which are inaccessable in CM directly)
6) export to KN5 and you are done
At any given time I want to do a deep change in shaders now I simply unpack KN5 in CM, do the change in KSeditor and go back to CM to make my shader adjustments.
I make it a habit to always "unpack KN5" in CM after any major shader adjustments to create a fresh persistence file which I then drop into my project folder (together with my Blender file, texture folder) so when I need to make an edit in the 3D objects or in teh structure in Blender I can go straight to KSeditor (loading the last CM created persistence file) and have all my latest edits perfectly intact.