I wouldn't use armory to scale models. When I made the "Enlarged" pheno years ago for NwnE, MDA modified the scale wizard to do mass scaling operations. I had no issues with any of the content that was scaled using that tool. The mass scaler is now part of NWMax Plus.
Without seeing the kilts you've modified I can't really tell you what the issue is with those particular models. You could try raising the Z-height manually in the files, using a text editor to do a mass search and replace with the corrected Z-height.