Default Omnirom And root

ive downloaded and installed the hammerhead omnirom nightly from their site and it works great except for the fact that my apps cant get root access. Anyone know why this is and how to get root access back.
ive also installed superuser, though when i go to install the latest binary through the app, the latest version of it (3.1.1) doesnt get installed, it stays with the default "legacy" version