The palette isn't being reordered. Here's some output from my fixed-up code, which I shall publish after a clean-up:

Looking trough my old posts in 8WAYRUN, I have found this: https://imgur.com/SD72FGz
I think I still have this tool in my archives, gotta be sure.

Hmm, interesting, the colors are not changed in the SC3 imaging format at all. Well, except or the Alpha.
Let me experiment in QT again, Let me see what results I get.

To elaborate: It is the good ol' PS2 swizzling. Here is the code I use for KH2FM which works with SC3 with a minor edit. The swizzling itself is as follows: QImage IMGD::Decode8() { QImage InputIMG = Parse8(); QImage OutputIMG(InputIMG.size(), InputIMG.format()); QList<QColor> PixelList; for (int y ...

I have already reversed engineered the VTX format completely. And I posted a semi-working code here written in QT.
I will post an updated unswizzling code here in 1-2 days, gotta clean up the code a bit.

I have even published some fruits of my work over on 8WAYRUN.