Same here, turned on like normal. I always noticed turning on the the amp would do a brief volume spike then mute. With or without the FBV MK II Shortboard attached.
Except now, no sound at all from guitar input. It appears many are facing this problem. One would think there would be a response after so many times of this occurring for so many years now. Really disappointed by modeling amps. It takes a lot of time to setup things for a reliable jam rig. Makes me consider going back to straight solid state amps. I love the Tap loop function and being able to turn FX on and off with the FBV ShortBoard Mk II. Never could get the Wah to work right. I think the activation switch in the ShortBoard is bad.
I'm going to try the Software route and see if anything repairs. But I doubt it. It seems like a system board failure and fairly common to these amps by design. Otherwise we would see answers here. I saw a video of a guy hot wiring to the CD input so that's a major warning to me about board failures. This amp has not been stressed in the least. The jack has not been abused in any way. I'm a veteran player and take a great deal of care. I know how to care for things. Some of my guitars are 35 years old. My 1990 Fender M80 Twin Chorus works great. It's just too loud for home practice.