I came here to ask a similar question. I just got a new One S black and its up to date. Unlocked the bootloader, rooted and installed CWM recovery.
I can run rooted apps fine, but I cant install busybox and ota rootkeeper isnt protecting my root when I ask it. Titanium backup shows its removing apps when I delete them, but when I reboot, theyre back again. Did I do something wrong when rooting, or is this just how the stock rom is?