I'm also experiencing the same issue. I purchased several H100x RGB Elite, installed the 1st one in a 4000x case with all 6 fans plugged in the Lightning Node Core and the pump in the motherboard 5v ARGB header. Everything worked fine, on an Asus motherboard using Armoury Crate Aura Sync.
However, I've now installed a 2nd unit in another computer running a Gigabyte motherboard and can't get the pump RGB to work. It stays white while plugged in a 5v ARGB header (tried all of them to see if they were defect, works fine with another ARGB led strip).
I tried a 3rd unit on this board to see if it was the pump but same result. Attempting to use the Lightning Node Core for the pump connection doesn't work at all, like others said, there's no option to select the device in iCUE lighting setup. Sounds like iCUE needs an update to support a 16 LEDs device.
All in all, great cooler for the price, but the pump RGB is quite sketch. I like the included 3 way splitter. In my scenario, I couldn't even plug it in a Lightning Node Core that comes with many Corsair cases because it's full with the fans and Gigabyte, ASRock offers terrible RGB lighting software (no Rainbow/ARGB effects).
Finally, I have tried using SignalRGB to control the ARGB header, however they don't have support for the unit (it's not in the list), and adding a custom RGB strip with 16 LEDs did nothing, it's stuck on white.
Conclusion, only works with Asus board, haven't tried MSI, EVGA or NZXT.