I had a Stomp, but I don't remember...is it also an interface? I know my Helix Rack is, but I don't use it that way.
If the HX is an interface, check your input gain vs. output gain in the global settings. Are you using as amp/cab block to process your guitar? If so, switch to preamp blocks without cab blocks for acoustic.
In your computer, do all of your DAW settings match what the Stomp is sending - sample rate, etc.?
These are the few things I can think of off the top of my head.
Other ideas? The best I can suggest is maybe a dedicated interface. Focusrite makes nice, little interfaces that sound great. You could get one and either DI box it to an input (XLR) or plug it straight into a line/instrument input.