You probably changed a different profile in the menus than the one you're using in-game. Just to cover all the bases (no pun intended), let me explain how to make sure you're using the right one - you'll only have to do this once, not every game or anything. I hope this doesn't come across as condescending, because I like to be thorough when I'm explaining stuff - you might already be aware of it anyway.
Choose the game you want to play on the calendar and advance to the team select screen where both teams' large logos are displayed. You should see a profile name beneath your controller. Make a note of that, because that is the profile that is associated with your Franchise team (you can change this to any profile from the options, but that goes further than I want to explain here).
Now back out to the main franchise menu and go to options, and then user settings (ignore what it says on "Current Default" for now). Once you enter user settings, cycle through your profiles with L1/R1 until you find the one that showed up beneath your controller on team select - that is the profile that is being used when you play franchise games with that team. If the settings under that profile are not what you expected, change them to what you want and then back out of options, making sure to select Apply Changes.
Go back to team select and the profile you had seen before should still be there. Go ahead and select that profile and team, and play your game. Once you're in the game, you can pause and make sure the options are what you want them to be.
That's a lot of explanation for a pretty short process, but again, I like to be thorough and this does seem to trip up a lot of people (it's an especially common topic around new release time). I hope that helps.
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