I have recently noticed the same, some things are much less volume through JACK than through ALSA.
A bit of a pre-amble before I continue.
I was studying music at school in the '60's and '70s, up to the end of high school, and singing in choirs as well as playing in school bands. Then in the '80s I was working in R&D designing MIDI equipment, and hanging out with bands. These days I'm a semi-retired computer programmer and sysadmin.
End of last year I stumbled across a MIDI keyboard Alesis V25 that a neighbour had thrown out. It had been sitting in a box outside soaking in dirty water coz it had rained and the box had other garbage in it. I pulled it apart, dried it, cleaned it, regreased it, put it back together, it works perfectly, and the lady who threw it out said I could keep it. I had been thinking for a while that I should buy something like this, read the reviews, lots of which used the word "durable", and if I had bought one, this model would have been on my short list. So starting New Years Eve (while I've been on holiday) I started learning how to play it (my previous instruments where flute and hand bells) and learning about all this fancy new music software that didn't exist in the '70s, plus relearning music theory. Including JACK stuff, and I use ALSA as the backend. BTW my holiday ends next week.
So I've been working on a cover for Pink Floyd's "Set The Controls For The Heart Of The Sun", to relearn musical theory, practice my new keyboard playing skills, and get familiar with the software. Mine will be titled "Set the controls for the drum and the bass" and I've modified the lyrics to be about climate change.
Couple of years ago I built what I call my super desktop, using a 64 core Threadripper and 256 GB of RAM. It has two sound chips on the motherboard, with several sound inputs and outputs, the video card has SIX (WTF!) audio outputs despite the fact there's only four actual outputs (two Display Port, two HDMI). On top of that I have a Plantronics RIG, which is a sorta mini mixer and USB sound device. So there's lots of audio inputs and outputs to play with.
END OF PRE-AMBLE.
I got to the point where I had to deal with getting the vocals laid down. I spend for too much of my time not talking coz I'm mostly typing to people on the Internet, so my old singing voice is very rusty, and delicate from lack of use. Also I have a small bedroom "studio", some cheap arsed microphone that came as a freebie long ago with something else, and lots of fans and air conditioning coz heatwave (37 C yesterday). So I decided to teach my computer to sing my lyrics. After much research trying to find pure open source singing things I decided to use Festival's inbuilt singing mode, crappy quality, but then I've only been an "electronic music producer" for a month, the rest of the music is also crap. This output a .wav file. So far so good.
FINALLY .... lol
Dragged this .wav file into MusE 4.1, it's both clipping AND very quiet. Huh? Plays loud enough in any ALSA software I try, but not in any JACK software. In particular VLC can easily switch between ALSA and JACK, so yep quiet through JACK, loud through ALSA. So it looks like it clips in MusE before it gets sent to JACK, then is quiet.
I have several other .wav files in this song already, none of them had this problem. I have recently noticed that some of the instruments I have been playing with are now less loud than they where when I first played with them. At least I think they are. It's entirely possible that between first playing with those instruments and now noticing they are less loud is the time I switched my JACK output to the other motherboard sound chip. Currently the ALSA is using the RIG USB output.
SOOOO it might be that this other motherboard sound chip is somehow incompatible with something about this .wav file and some of the instruments I'm using, but more compatible with the other instruments and .wav files. This may or may not be the same problem @LocProg has.
I need to experiment more. Switching hardware around between ALSA and JACK. Trying to output the .wav file with different parameters, or converting it to .flac first.