This appears to be a dxpack problem (ChooseOpponentWnd.dxpack). I had previously stated that
The last (xml files order) not randomly selected \MODS\ Sovereign (Unique Faction) does not show up in the "Customize Opponents > Available Opponents" section if said section has over 11 sovereigns.
Well, it seems the Choose_Opponents_ListGrid_Container (COLC) might be a good lead to follow. In the core file, COLC height is 625 while a normal Choose_Opponents_ListGrid_Entry (COLE) height is 50. Since the COLC contains your sovereign + at least one opponent, that's 50 + 50 = 100. Then, you have another 11 entry at 50 for a total of 11 x 50 = 550. This means the height is 650 > 625.
Now I'm not sure how the script works and why it shows all the sovereigns except the last one, but the 1+1+11 = 13 => 650 > 625 is explained.
I've created a new version of the screen that uses two columns (Quite ugly I might add) and 950 instead of 625 and was able to fit ALL my 35 sovereigns (None missing). Technically I guess I could fit up to 38, maybe 39, but I didn't test it.
Using that same height (950) but only one column, I ran into the same problem except the 1+1+11 turned into 1+1+18 with 1000 > 950. Hope that helps solve the issue.
LH Mods by Primal