There is a bug when creating Custom Civs which results in their selected custom images getting mixed up (the standard Civs don't appear affected). This existed in older versions of the game, but is still there in 1.6
It's a bit confusing to duplicate/explain (apologies for the length) but basically: I've picked all my images for a custom Civ and made all the relevant customizations to abilities/ships etc... and Save the Civ. This returns me to the Civ-selection window ("Choose Civilization") in the new-game-setup process. All looks good and as expected. If I then create/edit other custom Civs and eventually return to the Civ-selection window *usually* some of the images for my Custom Civs will get mixed up. To be clear: some images for individual Civs get swapped around - the images don't get swapped between Civs.
As far as I can tell, somewhere in the code the game should be looking in the custom \LeaderFGs\ folder, but instead looks in the \Portraits\ folder - and Vice Versa also. My theory is that since the corresponding LeaderFG/portrait files have the same filename (e.g. different "Borg Collective.png" in the LeaderFG and Portrait folders) it finds a file and uses it (so it might not always get noticed). However, since Portrait files are 128x128, using them in place of a 1920x1080 LeaderFG results in predictably ugly stretching. It also tries to squeeze a LeaderFG image into the Portrait box which also ends up looking wrong (not sure if this is due to the same script or if there is a second similar glitch somewhere else).
Also, in case this helps track down the culprit, if I've managed to create a number of custom Civs and they are all looking correct in the Civ-Selection window (i.e. at game setup), and then create another Civ where this problem becomes apparent, then simply selecting my previously ok Civs in the Civ-Selection window will cause their LeaderFG/Portrait images to also display the wrong images.
If I proceed into the game, the Portrait files are used in diplomacy windows of custom opponents (and look hideous obviously because it should be the corresponding LeaderFG file). I don't think I've had a game where my custom opponent Civs used the correct LeaderFG - it's always been the Portrait image. The LeaderBG image doesn't seem affected (i.e. always correct). The Logos image also seems ok, but not 100% sure.
I did a search and this (or similar) seems to have been mentioned previously:
Hoping it can be nixed.