superuser app is v3.1.3(46)
su binary v3.0.3.2(15)
-rwsr-sr-x root root /system/xbin/su
Automatic response was set to prompt now set to allow. still failing to update.
You might want to try the Superuser Update Fixer app from the Play Store.
Do you have busybox installed?
Were you prompted to allow Superuser to have Superuser permissions when you tapped Update?
Is Superuser listed under "Allow" in the apps section of Superuser?