I'm having this very strange problem with rooted devices: SU binaries are installed along with SuperSU and everything works fine. From time to time SU stops working until I reboot the device. If I open SuperSU I get the message saying I should install the binaries. Testing from shell SU doesn't work either.
I am not able to reproduce this reliably but I have noticed it right after reboot. So I turn the device on, SU doesn't work, then I reboot and then it does.
The device is running Lollipop and SuperSu version is 2.65. This matches the SU binaries version, I checked. Hardware is a prototype device based on a phone, not sure about the details though. I do know it has a Mediatek processor.