The issue is constant now. It seems like it just magically appeared and now it wont go away. Lots of noise, if you cant hear it in general listen to the delay repeats. It's very prominent for me. Im also getting a metallic (digital) type of noise when changing scenes while guitar stings are ringing out.
Everything is working fine here. Are you running a DAW while experiencing these issues? Any chance you've created a feedback loop with your DAW sending signal back into the preset via the In USB connection?
As for artifacts on scene change: with Axe-Edit III paused and changing scenes while playing using my FC6, I have no artifact issues. With Axe-Edit III unpaused there are hiccups on scene change as Axe-Edit III re-reads the state of the unit. This is a known issue and it's recommended you pause Axe-Edit if you need to improve scene change characteristics.
Try letting your guitar strings ring out or just be playing the guitar while you change back and forth between the first and second scene repeatedly.
You're changing channels on Delay 2 on scene 1 <> 2 change. Even with the algorithm being the same between the scenes, the parameters are changing quite by quite a wide margin. This can cause step functions to occur and you'll get audible artifacts. There are different ways to approach this. Easiest is to use a third delay block for Scene 2 so a scene 1 -> 2 change mutes the two delays and unmutes the third instead of changing the channel on an active delay. There are other options to make this work better than can be explored, but that's the easiest way to approach it.