You may have a weak preamp tube in the phase inverter. Like others have suggested I would start there.
Rectifier tube is active all the time but will be bypassed in 90W mode but will still be conducting current some current since the heater is also the cathode but the contributing current is negligible when it is bypassed by the quad of diodes. 10W power mode does use the tube rectifier to reduce the plate voltage for the class A (cathode biased pair of tubes, uses two 7W 360 ohm resistors). If the Rectifier is not operating properly the voltage will sag as if you turned the amp off but the LED's will be active since they are sourced by a different coil on the power transformer. The voltage bias circuit is also removed from the two tubes but not removed from the unused pair tubes since they are acting as a load ballast. Are you running 6L6 or EL34? If EL34 what type are they if not Mesa? If it was the tube rectifier, you may get the same result using 45W power setting on CH1 or CH2 with tube tracking selected.