TWRP says there is no root/superSU.. OS says differentlyu topic

I'm currently running the stock SM-T310 4.4.2 build. I have my device rooted (verified by Root Checker Basic) and I have SuperSU installed via Play (SuperSU Free v2.4).

Yet every time I am in TWRP and attempt to flash a rom, the ROM install fails immediately and at Reboot, TWRP asks if I want to install/fix Root permissions. What is going on and why is there a discrepancy?