Some of the DDS in Skullgirls work totally fine with various converters and viewers, and some are a giant jumble of mess.
Here is a sample mess. I've tried Irfanview, Noesis, Skullmod's DDS converter, and Nvidia's Texture Tools v2.0.8.
The file has NVTT and DXT5 in the header as well as DDS. Searching for NVTT brought up some kind of .dll file,
but I found this for DXT5. That might be why you're getting garbage.
The Vita DDS that come out fine also have all three DDS, NVTT, and DXT5 headers inside.
What do you mean by jumbled mess, the colors? This just looks like a normal DXT5 compressed file to me.
Could you upload some more samples?