First of all, thanks for the replies! However...
I think there has been a misunderstanding. I'm not creating new graphics. I have no talent at all for that. I'm just using some base and faction icon graphics from everywhere, and copying them into an existent faction file. For example, for the FTA, the Free Trade Association, I took Miriam's faction file, copied the PK faction emblem over their Cross emblem, and used the base graphics of the brian&sid-faction. So really, I don't see a way how the background colours could not be the same. Still, even the PK emblem with SMAC purple has a blue rectangle behind it in the game, while the believer file also in SMAC purple. So really, I totally don't see a what the problem could be.