I'm not sure why SuperSU isn't working as it should - have you tried manually re-installing the app (just the app, not the su binary).
Does a root checker app give you the all clear that you're rooted? If so I believe from memory there's an option somewhere in SuperSU for cleaning up to move to another super user management app. This might allow you to cleanly move to superuser without any problems. Hope I've remembered right and not sent you on a wild goose chase!
EDIT: just looked at my install of SuperSU and in the settings panel there's a section called "cleanup" offering the ability to reinsrall or switch to another super user app
Edited by flurry, 09 August 2014 - 07:08 AM.