The default is for presets to be altered when the controls are moved around. So if you go to a preset, crank the output knob, then exit that preset and return to it, the output will be cranked. You can change the default behaviour with Advanced Configuration. You can set the 'presets write protect' options to one of two things:
1) The default (left position), which is where presets are written over when you move the controls. Great for experimenting.
2) Write-protected (right position) where the controls affect the sound, but the preset isn't written over. Great for being able to mess around with knobs during a show, but have your presets not get messed up.
I suggest you check out the Advanced Configuration in the manual. It's got a bunch of goodies!