Ok, v1.92 is released!
https://withthelove.itch.io/pixelpalettetool/devlog/275924/pixel-palette-tool-v1...
It should address the garbled pixels issue and the crash bug when loading 16 color indexed palettes.
For the 'out of order palette' issue, it looks like this is an issue with the C# Bitmap API.
https://stackoverflow.com/questions/44835726/c-sharp-loading-an-indexed-color-im...
tldr; any indexed PNG with transparency is converted to a full fat RGBA 32bpp image by the C# Bitmap API which Pixel Palette Tool uses to load images. So by the time the tool sees the image data, it has already been converted to an RGBA image and the index palette has been tossed. Since there's no palette attached to the image at this point, the tool goes about it's normal process of extracting the palette from the image by scanning the pixels left to right, top to bottom. The result is that it gets the correct palette but not in the correct order.
As this is a problem in the C# image loading API, the only real solution would be for me to find another PNG loader or write my own. :(
The only silver lining is that the C# image API does seem to process indexed GIF images with alpha transparency just fine. So the workaround for now is to use GIF images if you want to load indexed palettes with transparency.
Thanks again for all your feedback and help ferreting out these bugs!
> SHIFT BY INDEX COUNT
Will work on this next. It shouldn't be too hard, the main challenge (as with so many features) is how to make it intuitive in the UI.