I encountered this bug after crafting my Onos. Applying my Warframe's color's applied properly everywhere except to energy, which remained pale blue. Going to manually select the color did change it visually on the Onos, but it did not remain after selection. The only way to get a change to apply was to select a color, then re-enter color selection and press ESC. Then the chosen color would be applied. This change did persist after leaving the menu for customization. "Switching weapons" in the arsenal caused no problems, however the energy color to reverted to default after switching to the upgrade menu of the Onos (I suspect the weapon gets "holstered" in the menu). Leaving the arsenal also reverts the color change.