Don't overthink this. The AD converters and the input section is really forgiving and the red light is not an instant "error" indicator. I find the red light is a bit irritating but I started to forget about it. You can turn down the clean sense a bit and the red light will disappear but if you don't hear any change in sound I would not care too much. 
Don't overthink this. The AD converters and the input section is really forgiving and the red light is not an instant "error" indicator. I find the red light is a bit irritating but I started to forget about it. You can turn down the clean sense a bit and the red light will disappear but if you don't hear any change in sound I would not care too much.
I was wondering if it has to do with my pickups, however they're not that hot (compared to active ones).
What has the clean sense to do with clipping the input? I thought it was only to 'boost' clean profiles?
The Clean sens has a dual function. It’s primary function is as a global levelling control to make clean sounds balance well with dirty sounds. This can be either cut or boost. I usually find I need to reduce clean sens other wise clean sounds are too loud relative to dirty ones. The secondary function is as an input gain control if the signal is clipping.
As Navar said though the AD converters are extremely forgiving (they have a ton of headroom) and it is really hard to make them clip. Try this as a test. Turn off all three signal chain blocks (Stomps, Stack and FX) completely. This will give you a pure sound without any distortion at all from the amp profile. Now turn the clean sens to Max. Is it clipping? You usually have to push it pretty hard to get any noticeable clipping. If it is reduce the Clean sens until the clipping stops. That’s the highest point you can go to without your clean sounds having any unwanted clipping. However, the AD converters also appear to clip quite gently so even when they do clip it might not be a major problem.
The Clean sens has a dual function. It’s primary function is as a global levelling control to make clean sounds balance well with dirty sounds. This can be either cut or boost. I usually find I need to reduce clean sens other wise clean sounds are too loud relative to dirty ones. The secondary function is as an input gain control if the signal is clipping.
As Navar said though the AD converters are extremely forgiving (they have a ton of headroom) and it is really hard to make them clip. Try this as a test. Turn off all three signal chain blocks (Stomps, Stack and FX) completely. This will give you a pure sound without any distortion at all from the amp profile. Now turn the clean sens to Max. Is it clipping? You usually have to push it pretty hard to get any noticeable clipping. If it is reduce the Clean sens until the clipping stops. That’s the highest point you can go to without your clean sounds having any unwanted clipping. However, the AD converters also appear to clip quite gently so even when they do clip it might not be a major problem.
I will try that Thanks for your answer, I'll keep you posted.
Wow ? those must be pretty hot pickups. None of my guitars clip that low.
You are right about the volume of clean rigs. Reducing the clean sens would make all clean rigs a little quieter in relation to dirty rigs. I presume you had to increase the level of all your clean rigs?
Glad you got it sorted though 
Yeah I don't use clean often in my band, so I'm not worrying about that
I have increased the rig volume for the 1 clean rig which I have in one of my performances.
About the output: I dunno man my guitar features '57 Classics which shouldn't be that hot...
I have tried your trick and maxed out the clean sense in order to make the clipping audible, then backed it off.
To be a 100% sure I have calculated in a safety margin, because my wah was causing the input LED to be red when playing in a higher position on the neck (or playing a double bend combined with wah).
I will try this out for now, if I ever have to change it back to 0.0db it's still possible. 
Any way thanks for your help, I'm glad that I know who the culprit was!
