If you guys have Gigabyte boards, the RGB fusion program screws with the cooler and causes it to not update. When I close it out, the update works fine.
You could set it up for lighting, but it won't properly work with video lighting since iCUE does not have more customization options for screen size yet.
If the cooler is still flickering with iCUE not running in the background, it may be a hardware issue with the LEDs. You could try setting it to a few different colors to see if maybe some LEDs are dying. For example, setting it to white should turn on all the LEDs.
When you're in iCUE and have 6 strips set in iCUE, make sure that your lighting effect is highlighting all the new strips. Just create a new effect to accomplish the same thing.
I would assume one of the pins, the PWM pin, isn't really making good contact. But yea I would try c-attack's suggestion #1, and try to really push the connectors together and see if that helps it.