JerryScript
Android Expert
While searching for a way to manually install the Superuser binary, I came across a Superuser website and found the binary file as well as the zip file for install. So I figured I would just try installing the latest version and hopefully that will take care of the problem. The only thing I didn't notice was it was the SU by DDChains. Phone started fine and went through the same Superuser's binary is out of date so I clicked on install, and then a window popped up asking for me to grant permission to Superuser. I clicked yes and low and behold, the original Superuser binary updated.
I snooped around to try to find a way to uninstall the SU by DDChains and found the Disable button and clicked disable. Now Superuser seems to be working just fine. My questions are, could TWPR be messing with the phones root when is tells you that root has been lost, after flashing a kernal, would you like to fix and I select yes? And 2, is it OK to leave the SU by DDChains installed but disabled?
Yes it is possible TWRP was messing with your su binary, but it usually doesn't cause issues.
The easiest way to uninstall all other versions of Superuser and install Koush's version is to run his zip file, which can be downloaded from the bottom of the description section of his app in the Play Store. Just open the store, search for Koush, choose the app with the # icon, expand the description section and scroll down to the bottom, then click the link for the flashable zip file. This zip file will uninstall pretty much every version of superuser before installing it's own binaries and apk file.