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The Helix models are based off the amps and effects in the Line6 labs. You can line up 10 fuzz faces and they will all sound a little different. The model in the Helix is modeled off the one in their lab. That's just one of the 100 reasons your results will vary.

Does the sound happen with no PC connected via USB or with the Helix in a different room or different location (someone else's house)? I've had weird sound anomalies like that come from the USB connection to my laptop or harmonic noise coming in from the AC Power I was plugged into.

I haven't been on here for a while. Nice to see things haven't changed. -- O |..| \____/ ^ ho-made emoji

Page 53 in the users manual

It's not an issue on the Helix Floor model. It has a mic input, headphone jack, separate headphone volume control. Doing what you are explaining is just plug and play with the Floor model.

Get yourself an external expression pedal so you can run two at the same time. I use Helix Floor with two external expression pedals. I use on board pedal for volume, and the other two for various other effect parameter control. You don't need to spend a bunch of $ either. I use the plastic Line 6 EXP-1 pedals. Had them for years with no issues.

Helix is not capable of polyphonic pitch shifting at the moment, so it does not do drop tuning very well when playing more than one note.

I do this by saving presets with combinations of amps/drives with specific settings. There are 1024 user presets available, plenty for me to save a bunch of amps and drives that I love. I call one of them up, "save as" in a different location, and add modulation, verb, delay to taste.

Does it do this on a fresh (empty) preset that you have never modified?

YES!!

Probably something on the DAW side. I have no issues (using Reaper). If you start a preset from scratch, just put an amp/cab block in that preset, do you have the same issue? If so, is your input pad on in global settings?

Unfortunately the low frequency oscillator in tremolos do not reset on the rising edge of playing a note, they just run continuously. I tried the "throbber" and it doesn't either. Your best bet would be to synchronize your click track to your Helix. with both set at the same tempo, play a note to let it oscillate, then start your click on the beat of your tremolo.

I haven't noticed this one. I leave my Helix on for days at a time and no issues with reverbs not working. Maybe certain reverbs?

some delay models have a max delay time of around 350-400ms, no mater what tempo you tap.

make sure global EQ is turned off on the Helix. If it's on, eq settings will be affecting the sound at the speaker

If you are looking to achieve your "ideal" clean and overdrive tones with a single preset, using a strat (stock PUs?) and Ibanez (with active EMGs)?

Yep, do a complete factory reset/restore. It will be squeaky clean, then you can restore your backup. If your backup still contains some corrupt presets, they will get restored back to the unit. So, you may not want to do a full restore unless you know you have purged the corrupt presets.

You may want to mention what unit you are using, what you are monitoring your tones through (FRFR, "real amp" etc...), instruments you are playing, etc...

Can you post a pic of the signal flow of your preset?

This. reload your preset before playing.

Floor model running 2.82 running 10 stomp mode. Foot switch 10 was assigned to change four different amp parameters. Foot switch 9 was blank. Used the capacitive touch on 9 and 10 simultaneously to switch positions. When I hit OK screen goes blank, screen backlight still on, unit is completely frozen but still outputting sound when I play. Had to cycle power to get back to where I was. Tried to swap 9 and 10 again, locked up. It was repeatable every time. I had to go in and manually set foot switch 9 on each of the 4 amp parameters to move them to FS9.

Do a quick search about this subject in this Forum, you will find many posts about it.

Global Settings> Ins Outs> USB in 1/2 Trim

What Helix input are you plugging your bass into?

For me to get that percussive strat "spank" then the nice bell tone, it is all in my picking. If you are light on the picking, you won't get that sound. Pickups will effect that as well.