Interesting. I have been testing with the auto subs lately.
What I discovered was that when setting auto subs in "my madden" and saving to your profile and then exiting, they all go back to default when you return ! I know about using the start button to save and my profile was properly loaded when I came back to the auto sub section. This has happened 2 or 3 times : every time I set them and save, they go back to default the next time I check them there. This happens only in the"My Madden" section, not in the on line CCM. This is most likely another bug. Ironically, however, this may be what caused proper subbing for you in your off line experience.
Maybe - and this is just a wild postulation - the default auto subs will work to better achieve proper substitutions than the custom sets we have all used in the past and continue to use today. Perhaps auto subs aren't actually broken, but are now working in a different (lower, and closer to default- as SEC discovered) value range than what we have been accustomed to.
I am going to explore this further.