So when your not using SC, is the SSID name the same across all radios while in manual mode?
I would do the following, change the SSID names across each radio to be different.
What happens if you set 5Ghz radio 1 to 36 and radio 2 to 149?
Please post captures...Seem the channels you set and what is being reported by the scanner is not coinciding for some reason.