It is established that you have a major problem and lots of good advice. I would do the following in order:
1. Check that Wah is not engaged. Check cords you are using to go from Helix to amp. Try new ones. If using XLR make sure they are balanced cables.
2. Turn off Global EQ
1. Back up your IR's and export your bundle to save everything.
2. Update to latest firmware 2.01 and make sure you do the last step of rebuilding your presets.
3. Try different factory presets to see if problem is gone. If it is, load your bundle and IR's and go. If not you have a bad unit.