Having the same issue. I have my game on the C: disk and my documents on the E: disk.
For some reason Titanfall decides not to save a config file anywhere, causing me to change my settings everything I start it up.
Changing my documents folder to the C: disk does not solve the problem.
Dead Space 3 saves fine.
I seem to have figured out the problem I'm having (with both Titanfall and FIFA 14) myself, hopefully it will apply to your situation too. When I moved the location of 'Documents' to my other drive using the 'Location' tab in the settings it was originally moved to my G:\ drive. After I swapped out some HDDs and changed the letters of my drive (In this case, G:\ to E:\ ) that contained the 'Documents' folder, Windows lost the original path to the default location. Since Origin uses the default location of the 'Documents' folder to store data which now no longer exists (G:\Documents) it could not write any settings to the folder. I found a tutorial to restore the default location of the 'Documents' folder back to C:\ and then moved the location back over to E:\ where all of my actual documents are and it merged the folders. Once I relaunched Titanfall, it gave me the error message of my cloud saves being out of sync then proceeded to create the Titanfall folder in my 'Documents' folder when the game synced and launched. Now it seems my settings are saving and it even fixed my FIFA 14 crashing issue. Hopefully this will work for you too!
http://www.sevenforums.com/tutorials/18583-user-folders-restore-default-location.html - Tutorial to restore default 'Documents' location, use the second option involving registry editing.
Let me know how it goes!
