FX Loops are problematic in amps … the input peaking LED could be due to a resonant peak caused by a reactive impedance mismatch. Have you tried placing a buffer pedal as the first item in your FX chain? This may help you by creating a broadband impedance match for the amp's FX send, and the inputs to any FX tied to it.
Give that a shot, I am betting that will clear this annoying problem up. If you have a Boss EQ pedal, that has a buit in buffer. There are dedicated pedals that will do the job.
The best of luck to you!!!