Could you share what you did to fix that?
I'm having the same problem (skies in some of these wads, like ACHRON22, not loading).
For the life of me I can't figure out how to fix it.
It's suspicious that, when I run "wadsmoosh.exe", the output is a "pk3" folder, and not a file... I can pack it up into a .zip file and then rename it to .pk3, but, maybe the mistake is somewhere around that?
I'm completely stumped at this point. Any help would be greatly appreciated.