Bump because I'm having the same issue. I'm trying to replace the files for Ferrothorn with Ferroseed's as a test, but when i repack the files with Kiwi all of the files are jumbled up. I don't remember having this issue a couple years ago when I used it on BW, but now I'm using it on BW2 and this is happening. My method has been just extracting the files within the a/0/0/4 narc and copying and renaming Ferroseed's files to overwrite Ferrothorn's, then creating a new narc with Kiwi. When I check on consoletool, everything is messed up. I also tried with Tinke and the same thing happened.
