When using AmpliTube 5, I'm using a slash boost pedal, and a treble boost pedal. I'm also usually sending as much gain as possible to get a decent sound. By that time, if its not clipping, the signal to noise ratio is so high that the buzz or hiss is really loud and almost as loud as the music.
On some amps I'll have the track gain knob turned up 10db or so. Then I'll turn the input way up in the software. With output near zero depending. Without these steps everything just sounds muffled.
Amplitube 4 didn't have this issue.