The way that this works is that Adventuron takes the image, allocates each new RGB combination to a palette slot. It uses up to 255 slots for 255 different colours (the next needs one colour for transparency).
After it runs out of 255 colours then colours are matched to the closes existing palette colour. That algorithm is pretty basic, and most people won't have to worry about running out of 255 colours in pixel art graphics.
From there, Adventuron converts the images to PCX image files (supports up to 256 colours palettized). There is no colour conversion during the PNG to PCX conversion (assuming < 256 colours).
DAAD Ready then uses a tool called "SC2DAAD" to convert the PCX file format to NXT file format. I assume that's where the mapping error is occurring. If there is a concrete example of the graphics being badly paletted then I'm sure Uto can take a look.
Chris