Edit: Figured out the bug. On the affected skins, the primary energy color is determining the color of the emissives. Primary and secondary emissive colors can change its brightness, but not its hue.
Affected skins I've found:
Daikyu Ormolu, Tipedo Ormolu, Phantasma, Hecaton Shotgun Skin, Snipetron Vandal, Soma Huntsman Skin, Cernos Prime, Nidus Night Hunter Skin
Did some code get reverted to back when we only had one energy color channel?
As of today's mainline patch, Ormolu skins are ignoring the chosen secondary emissive color. Tested on Daikyu and Tipedo.
Edit: Also Phantasma, Hecaton Shotgun Skin, Snipetron Vandal, Soma Huntsman Skin, Hema, Cernos Prime
Looks like some skins are using the second color, but only barely. The primary emissive color is completely overpowering the secondary, no matter what combination is chosen.
Nidus Night Hunter is using the primary energy as an extra layer over the primary and secondary emissive channels. If primary energy is set to black, the emissives don't show at all.