Try setting SuperSU to Prompt for Greenify and reboot the phone. Did you recently update either of the two apps or your ROM? What versions of them are you using?
Sure. I was using Greenify for years without problems. I have rooted LG G3 (Stock Rom, 5.0). Today I opened the app and instead of usual interface I got the "Welcome to Greenify" screen.. pressing Next on this screen opened new screen where it asked me if my device is rooted.. I said Yes. Next screen checked root privilege and after a few moments the app notified me with the red text:" Root privilege is not granted. Please grant it manually in the root management tool/settings.". Well, OK, I went to SuperSU and surprise, it's already granted. The problem now is that Greenify doesn't let me past the cheking root privilege screen since the "Next" button is grayed out so there is no way of using this app. So... what's going on.. Greenify worked for years and now this bull. I have no idea about moving apk's and all this stuff... why it suddenly doesn't work anymore?