Hi,
I’m thinking along the same lines as “SaschaFranck” with this one. Are you actually talking about “Snapshots”, or changing “Presets” here?
If you have a sound ringing out, and providing you have “trails” turned on for the relevant FX blocks, there should be no muting happening. Zero, zip, zilch, nada, nothing.
If you mean that you are actually changing “presets” then there will definitely be an audible gap as the Helix ditches one set up and loads another. As of v.3.0 firmware this gap can be avoided, but at the expense of losing one path of DSP. Probably not what you want to do. Although, IIRC, I read a post from Digital Igloo who stated that the time between switching presets was in the region of 50-120ms.
The only other thing that I can think of is that maybe something in your Snapshot setup is interfering with a bypass On/Off state.
Also, when stuff gets weird, do a factory reset and rebuild your presets!
Hope this helps/makes sense.
EDIT:
Post an example of a preset with the misbehaving snapshots for others to check out.