Because the faction logos seemed ot cause this problem, should I redo the troublesome logos using SMAC palette colors, or is there some other issue going on that needs ot be fixed in some way? (Or am I just indexing to the palette in the wrong way.)
faction.pcx has a special palette, unique to anything normal and even to faction2.pcx and faction3.pcx.
To save a palette, you may need to enable the palette dialog box. Hit the left arrow of the "Layers, Channels, Paths, Undo" window, then "Add Tab", then "Palettes" (screenshot for clarification is included).
Then right click the Palettes dialog, then "Import Palette...", and import from the image (you must have it open to do so).
Remember to use a palette for faction.pcx, and a different palette for faction2.pcx and faction3.pcx (they use the same palette).
Hope that helps. Any more questions, I'd be happy to answer. I'm pretty good with Gimp.