Doesn't recognize Root on CM 12.1

[ghctim]

I have installed the app on CM 12.1 and I have granted it root permissions but it doesn't recognize this. When I try to install it tells me I must grant it root access but when I look at the APK permissions in CM12.1, it is already granted root

then I installed it as a system app and I am still getting the same error

[ghctim]

I got it to recognize root but with stock recovery, it boots into recovery and doesn't actually install the package

[mfonville]

stock recovery doesn't support the 'install-mode'; did you try with TWRP already, or does it not recognize the root then anymore?