What signal are you sending to the H90? What is your signal chain before the H90? It should be easy to see the clipping LEDs by connecting a loud synthesizer or drum machine to the H90’s inputs. A guitar or bass will be more difficult since the signal is much quieter.
Do you have any of the Program/Preset input gain parameters turned up on the H90? The clipping LEDs are pre input gain parameters, so it may be that you’re not clipping the inputs and you are clipping the signal somewhere else in the chain.
I’d suggest loading the User 2 list and testing the levels of your setup with an INIT Program.