Marshall JCM800 strange behaviour

My Marshall JCM800 Kerry King signature has a led on the boost switch that is red when no signal is coming in and green when you have signal
Lately it started behaving weirdly (since I have started using a Peavey T-40...)
- if I stop the strings, it becomes red as if the bass was unplugged
- while not playing, the led flashes occasionally between green and red as if I had intermittent signal
- when connected through the ABY switcher, and I DISENGAGE the Marshall amp, if I use the tuner BEFORE the ABy switcher the amp led turns green (this is the weirdest and makes no sense at all and may even be a separate ABY switcher problem )
My main concern is that the amp may be damaged by these things, what could possibly be? Should I worry about that?

 

thanks a lot!!

 

I'm using two Ampeg PF (410 and 115) on the bass signal and a Fender Supersonic 2x12 for guitar
Yeah I read about the crossover, but actually I like how the KK roars on the lows (and it has some HUGE lows for a guitar head!)... So I'm not sure I'm willing to change that, both me and my drummer are liking a lot the sound right now (I'm a little bit less satisfied with the "bass" side but that's another story... I'm planning to try different head and cabs)

 

Anyways I hope to perform some troubleshooting (based on suggestions from the Marshall forum guys) tonight and tomorrow. I think the problem is the bass.