Just seems like your root or busybox is messed up. A couple pages back I posted a rasbean extras file. You could try to reflash rasbean and then that extras. In there select busybox. That will actually install the supersu, su, and busybox and set permissions. Reboot and see if that might have fixed whatever went wrong.
Edit: oops I did that for the nexus7. Never posted my nexus10 one. Could tmr. But I think you just need to reflash.
Thanks for the reply.
I did reflash and that didnt help out. (With adaway problem)
I had the fix permissions problem since the first build of RBJ but everything worked great even adaway.
Now every root app is working properly except for Adaway (or similar apps )
Edit: for some reason adblocking works now. But I still cant fix permissions.