I have the N900A that I rooted using Kingo Root. No safestrap or new roms, just rooted. I obviously had the 'Custom' icon.
At day 20, my phone wouldn't charge any more or be recognized by USB. I tried everything. Factory reset, cleaned the port, cleaned the cables, new cables. Nothing helped. And it would have to be warranty exchanged through AT&T, but the warranty was voided because of root. I couldn't use Kingo to unroot, because the PC wouldn't recognize it.
I was able to find a workaround, using this:
In fact, I really only used the third step. I didn't download or flash the rom. By some miracle, the PC would connect to the phone when it was in download mode. I used Odin to flash those four files, rebooted, and the custom icon was gone.
I'm hoping that this has removed all trace of root from the phone. The knox counter is still at zero.
I thought I would post this in case anyone else had a similar problem.