Always remember that there are many different places where you can increase or decrease gain on the AX2 and AxSys. If you’ve chosen to increase it in all (or even most) of these places, you could be causing clipping after the TubeTone modeling. One of the most
likely places for this to happen is in the Graphic EQ. A quick test is to turn the EQ off and see if your sound cleans up. If it does, move your whole EQ curve down so that your highest frequency boosts are no higher than +6. A general troubleshooting procedure to find where you might be getting unwanted clipping is to turn off all the effects, make sure that the sound is clean, then turn the effects back on, one at a time, checking for clipping after turning on each one.