You should have the proper palette selected, from the XCC palette menu list, when you extract a shp as pcx. Possibly when you extracted the base images you're working on, you had the wrong palette selected?
The palette ordering options are just view options, to help you find the color you might want to use. They don't affect the palette index values. To do that you would have to actually edit the palette.
Generally, you want to use 'nearest color matching' when first applying a palette. However keep in mind that certain identical colors might get mixed (like the prog uses non-remapable reds when it should be using remapable reds). To avoid this, use 'maintain indexes'. This does what it says, it maintains the indexes.
'Error diffusion dithering' is only used when applying the palette to a 24-bit image, and usually not even then. Try it and you will see why.
This image uses 'nearest color matching' for most of the C-GEN frame of the image, but a portion at the top left hand corner was done with dithering, since there were no colors on the palette than matched well.
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