Line 6 know this problem since May 18, when I submitted this bug and they acknowledged it.
And yes, they still didn't resolve it after almost 4 months.
It drives me mad that an annoying bug like this one take that long to be fixed.
By the way, I think you're using MIDI over USB? In my experience with the Helix, MIDI via USB is far less stable than MIDI via MIDI cables, and that particular bug doesn't occur with MIDI cables in the MIDI In/Out ports. Also, if the Helix is connected to a computer to send MIDI signals via USB, and the computer is connected via an USB soundcard to the PA to launch samples, use virtual instruments, etc, if your electric system is not top notch, there will be a lot of noises. And those noises are disappearing when using MIDI cables instead of USB.
(Also, on a not-so-far topic, I'm pretty pissed right now, because I found plenty of these bugs, and I lost a lot of time because of them, and now I've got two options: loose lot more time by trying to reproduce them, identify them, and then submitting them one by one to Line 6 - Line 6 that doesn't seem to be quick to fix them anyway, so why bother? -, or selling the Helix and try another setup. People at Helix team: you've got a great concept, you should not allow that many bugs - better test procedure? -, or at least, you should be really quick for fixing them. At this price point, part of your customer base are professional musicians, when you can't save a preset and restore it because when it's restored the snapshots are not restored correctly and it destroy your preset, and even in some cases make the Helix freeze, for frack's sake!)