I'm getting this also, few things:
First it only happens in Cyseal. If I go to Homestead, Black Cove or Luculla, save there and reload, then I have whatever character I had selected when I saved. If I go to Cyseal, doesn't matter which character I save with it's always the "second" character that gets defaulted. I assume whenever the bug occurs it "locks" that particular zone but not the others.
Second, I believe this is linked to saving then reloading during dialogues or events. I'm not 100% sure but I think the game believes you're still in a dialogue and default to the character that initiated that. However it seems curious since I almost never initiates dialogues with my 2nd char but I believe one time I had the Fabulous Five recruitment dialogue start when I had the 2nd char selected, saved since I wanted to make sure I had the right traits bonus from the questions and it broke. However talking to him again with the other character, saving and reloading fixed that particular save.
I couldn't reproduce the fix though on my most recent game, I'm not 100% sure which dialogue broke and so I can't check if my theory is right.
I've obviously tried a lot of stuff to fix it otherwise, breaking chain, recruiting henchmen, moving far away from each other, having one character dead, saving in combat, saving in dialogues, changing group formation, changing group position, leveling up, completing all the quests I had when it started bugging, using the actual save/load buttons instead of quicksave/quickload, quitting to main menu before reloading, restarting the game before reloading and such, none of it worked.
Gender definitely unrelated, I play with female/female combo. In case of though, the bugged character that defaults everytime is the one on the right on the char creation, when I usually use the left one to lead.