Make sure bot radios do not have the same SSID. I use _2 on the 2.4ghz SSID at the end of what I have named it. 5ghz, I just use the same name as 2.4 but without the underscore or number (i.e. home_1981_2 for 2.4, home_1981 for 5).
Set the channel to static number 36 - This resolved my issue. Auto feature seems to bugged but never used to be, but I've commented on this before and still get told that nothing had changed in the firmware build. I was affected on a RT-AC68U and RT-AC3200 - However when I dropped to Asus's official firmware on the RT-AC68U they had fixed the issue with the 5GHz disappearing, in their release notes.