I realize this is an old post, but I found a solution and this thread was one of the few that popped up as I searched around.
In case anyone is still having this problem, I saved over the default profile with my custom settings by:
1. Make all the custom settings you want and save it to a new profile
2. Show hidden files and navigate to C:/ProgramData/Asus/DIP/FanXpert/Profiles where AI Suite saves all profiles.
3. Rename the profile file "Standard (ASUS)" to anything else, and then rename the file that is your custom profile to "Standard (ASUS)"
4. Reboot. AI Suite will load "Standard (ASUS)" that now contains your custom settings