This post is several years old, but I'm glad I found it because I thought I was nuts.
Same issue. It seems like some of the commenters here don't understand what's going on. It's like playing a guitar with extraordinarily weak pickups. I'm not even talking about a vintage 50s strat with pickups that need to be rewound. Weaker than that. It makes everything sound and feel horrible.
Let's say I find a YouTube video in which someone is building a preset. I follow along and do everything they do. They're playing a strat. I'm playing a strat. While I'm sure there's differences between our pickups, they ought to be in the same ballpark. But they're not. To get a similar sound I have to put a gain block in front of everything set to a ridiculous 9.5 or 10 db.
This is an input gain issue on the Helix hardware devices. It's not an output issue. When I go LT or Stomp into my interface I have VU meters and they're green occasionally peaking to yellow, but at the same time it's like the modeled blocks inside the Helix are starved for signal. Overdrive and fuzz pedals don't sound right. Amps don't sound right. If you just crank levels you get closer, sort of, but not really. Nothing responds right, plus it gets noisy with single coils.
Guitar pad is off. Remove the cable going into the HX and plug it into an amp and all is right with the world so there's no issue with the guitars or the cable.