Strange. I've never seen that before with this unroot method. Strangely enough my 4.3 update came even though I was flagged custom. Usually it dissapears within a few minutes or several reboots. Of the unroot. If it doesn't dissapear, the only thing I could think of is to re root with that saferoot method in the first post of that thread then do the unroot again to make sure it does it completely. I'm guessing soemthing didn't go in the few times you might have tried. The SU binary is all that is really needed for the root itself. SO if that is not there then yes you are unrooted, but if something else lingers like busybox it would still trigger the custom flag. If this doesn't work. I would try odin. I have never used ODIN for the I337 before so I can't give you any pointers there.
I did have my 4.3 rooted with saferoot and unrooted to get the kit kat update if that gives you hope.
Sent from my GT-P5210 using XDA Premium HD app
AT&T I337 Galaxy S4
NB1 Kit Kat Firmware
Work around Rooted (Thanks to all who worked on that method)
Galaxy Tab 3 10.1 GT-P5210