apps greyed out after installing android pay?

As title says. I installed android pay. I went through the setup which changed an nfc setting from sim card to processor. Then I restarted my phone. About 6 apps are missing. If I go to settings/ application manager/All. I can see them there but they are greyed out with an SD symbol above them.
Annoyingly this includes "suoersu". Android pay doesn't work with root so I was hoping to turn root off temporarily. I can't uninstall supersu, install it from the playstore or from apk. I can't even install other versions like superuser etc.
Any idea as to what's going on greatly appreciated.
It's a galaxy S5 with xtrestolite rom.

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