I found a way to beat the Samsung warnings to say the phone has been tampered with / custom binary (you see this in Download Mode, turn the phone off and press Volume down, Home, power on - volume up to view your status)
I had rooted with
ChainFire's auto root, installed
Super SU by ChainFire via the Play app store to get further updates without having to flash with Odin.
EDIT: After installing Super SU, open it and go to the settings and install Super SU as a system app in /system - this is the part that makes this "trick" actually work.
I had done this weeks ago, since the UK nonbranded 4.1.2 firmware was released - Triangle away only ever got rid of the red exclamation mark on boot, but the flashcount was always 1 and I wasn't that bothered really.
The last few days my phone had been playing up, I'd installed lots of crap and been testing beta apps and it kept freezing / rebooting itself, so I factory reset it after playing with
Koush's Carbon Backup (going to test the restore later on)
Lo and behold after the factory reset and initial configuration process, I noticed the phone automatically installing updates to system apps via the Play store - quite normal really, except that one of these apps was Super SU ! Weird I thought... so I installed a root checker, to see if I still had root. I did! After a factory reset I still had freakin' root! and download mode says it's all Samsung official / 0 flash count
Just a thought I'd mention it in case anyone else still wants root and wants rid of the warning in download mode so you don't have to argue with your network provider if you send the phone in for repairs that's it's actually FINE to root / jailbreak your phone in Europe and they can't easily refuse to repair the hardware because of it.
