This may be due to an IR (Impulse Response) being present in your signal chain. Some IR samples have higher natural volume levels and should be turned down using the "gain" parameter on the IR page.

If you are not using an IR but still hear clipping, you can adjust the full rig’s level at the rig output by pressing Output in the bottom right corner of the HeadRush Pedalboard’s display and using the top-most knob on the right of the display to turn down the rig volume until the clipping is no longer present. 

If using a third-party multi-fx/amp modeler, refer to its user manual for a similar process if necessary.