I have the exact same problem on my Helix after updating it to 3.01.0.
After hearing that the spillover mode will be available I edited all my presets so they only use one path.
It works without any problems, but somehow after a bit of a time the same problem as yours appears.
If I switch the preset -> no sound
pressing the footswitch again -> sound
pressing it a third time -> no sound
and so on.
I absolutely don't have any clue how to solve this problem.
EDIT 2021-02-07:
Today the problem appeared after I used the tuner instantly after starting the helix (I didn't play a single note between starting the helix and using the tuner).
Then I restarted the helix and didn't use the tuner and these problems didn't appear at all.
