It's not about the instrument, it's a problem with the Helix, it happens with all the instruments I plug in and it only happens with the Helix, I have other equipment that remain normal. Test your unit please and let me know if the same happens.
Every presets, every guitars, not only on my HX stomp unit but I also identified the problem on other Helix units from friends (Helix LT, Floor and other HX stomp). I now believe it is a failure of the equipment
my hx stomp sounds totally out of tune when I play notes after the ninth fret, for example: when I play the note B on the ninth fret, it sounds along with a C# note