After rereading your post I was confused by what you meant when saying "set the fill up to 100%." When updating your SGII you should be updating your gallon fill total by actual gallons and not by percent filled.
Example: Using the side buttons to adjust the fill amount to 10.2 gallons if that's what you put in the tank. Not adjusting the percent numbers to 100% if you completely filled the tank.
The calibration of your scanguage is a work in progress before your first fill up. Usually after a fill up or two you will have adjusted your gallon fill numbers enough to be close to your actual mpg (and when you fill up again and again you should not be far off from what the SGII screen says you filled up). There is a thread on this site where guys have posted their percent adjustment for specific vehicles which might help starting out if you want to do a search but once you have a couple fill ups you should be close to your actual fill mpg.
If you're still way off after a couple fill ups check your settings to make sure you have it set for the correct engine size, engine type, tank size, etc.
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