I changed my battalion and now I can't get Lowest to Highest deployment to work.

I'd previously played 200 games with my last battalion lowest to highest.

I've set the setting Lowest to Highest, pressed B to save and exit and reset my console a solid 20 times now only to see it Highest to Lowest when I turn the console back on and check settings.

I'm getting quite ****ed. Any ideas?

I've been getting the same problem.
It's not saving for every setting you can change. I've tried changing it, saving the game after playing a match in single player, saving a replay, deleting a replay, basically anything to get EndWar to mess with the hard drive and it just doesn't want to save the settings. It saved the first time I played the game [changed sound all to 3, brightness and contrast] but now it won't save any changes.
It may have started after associating my account with my ubisoft account, I'm not entirely sure.

I had a similar thing happen right before my hard drive failed. I had to buy a new hard drive.

So did yours start saving the settings after the new hard drive?