Do you have the analog input gain of your H9 turned up?  You might want to check your signal levels by clicking on Pedal in the bottom right hand corner of H9 Control and going to the Input Gain and Level Meters section.

I have checked and it is set to zero. Can the input gain be saved per preset, or is it just the output level? (I don’t have access to it using an iPad at this time, I’m just using the Windows version of H9 Control via a USB connection).

I’ve tried a few different guitars now (I work in a music store, so I’m letting the staff try out the new presets on my pedal). On a couple of Tele’s, the clipping isn’t as bad. All of the other CrushStation presets seem to behave as expected. It is just this one preset that the clipping is really prevalent on. I’ll do more troubleshooting and try a few more guitar combinations. I’ll see what I can find out. I’ll also have my iPad back by tomorrow, so I’ll be able to do some real-time parameter tweaking.