Updating ruined mine
I was in the same situation as you until today. I got kitkat on my SM-N900V, then used towelroot (which is amazing!). Then when I would open supersu it would ask 8 out of 10 times to update the binary. I tried normal and CRM/whatever and neither worked. Then, today, when I opened supersu, it said "Update successful, please restart" so I did. After the restart, when I went to open supersu, it would not open, and just freeze until I hit the home button, then everything would be slow and laggy. I restarted my phone, and then supersu would open, but would sit with the spinning loading wheel loading the root apps, and never load. I opened Titanium Backup and it froze on "checking root rights".
To make matters worse, I had just enabled pry-fi, which needs root to spoof the MAC. I was just trying it out, but after supersu updated the binary, pry-fi would freeze on asking for root. So this broke my wifi. Now I am on data only, and supersu doesn't work. Any root app freezes.
I would not recommend doing the binary update, it might have ruined my phone.
PS: I ran towelroot over and over, restarted, ran supersu (sits loading apps), ran towelroot, tried pry-fi, etc, ad-nauseum, nothing helps
I am considering another factory restore... Don't do the binary update, just keep trying supersu and one of these times it will let you in without asking for update.