I won't say that I don't hear it... I do hear a certain amount of fizz or hash or whatever you want to call it, but I don't find it all that objectionable. I hear the same sort of thing if I plug a guitar with humbuckers into a Fender amp a lot of times, too, though. So I guess my feeling is that there are some people who seem to be really bothered by this for whatever reason, but thankfully, I'm not one of them.
One thing I would ask that original poster is if he tried switching Input 2 to something other than "Guitar" or "Same". That would make a difference in the gain staging through the unit, definitely.