Pierre-Luc, you are cramming a *lot* of information between the staves which 
is stacked vertically, and I think this is the cause of your problem.  You 
could experiment with commenting some of it out temporarily and seeing what 
happens.  My comments below are based on a philosophy that the sheet music 
should only have the information the musician needs and nothing more, to make 
it as easily readable as possible.  Extra text could be confusing and 
distracting.

For example, thinking as a musician looking at this I would not need the Intro, 
1er Couplet, 2e Couplet, 1er Refrain, 3e Couplet, etc., at all.  I would just 
need to know what notes to play.  Removing that text will remove at least one 
vertical line space.  There's one spot where there is a time cue, part cue, 
ritard, a tempo, bar number and chords all stacked on top of each other

Do you really need the time cues on the individual parts?  That's another 
vertical space between the staves.  Is the bassist playing to a clock (e.g., a 
soundtrack cue synchronized to a movie)?  If not, is the tempo specification 
enough?  64 bpm = .94 sec per quarter note, so your time cues automatically 
work out- although the ritards will challenge that.

As for the chords themselves, unless there is improvisation do I need them as 
the bassist?  If the part is only to be played as written, the chords might be 
unnecessary.  If there will be improvising, then that's different.

Suppressing the bar numbers or only having them at the start of the line will 
reduce visual clutter.

Should there be an initial barline or a double barline between the Intro and 
the 1er Couplet?  That would make things look a touch less confusing.  Speaking 
of the Intro bar, something is odd there with notes preceding the bass clef and 
time signature.  I don't know what to make of the two notes with a vertical 
line between them.

All that being said, if you do want to keep all of that information then 
forcing Lilypond to increase the vertical space between systems may help.  
https://lilypond.org/doc/v2.25/Documentation/notation/vertical-spacing

> On Nov 30, 2025, at 9:53 AM, Pierre-Luc Gauthier <[email protected]> 
> wrote:
> Hi there,
> 
> I still get unexpected chords crammed inside the staff. I'm so unsure
> why, and so randomly. While writing the part, I often have the feeling
> that everything is ok and then, for some reason, LilyPond gets thrown
> off by something and, from then on, it totally disregards the chord's
> vertical alignment.
> 
> I do not yet have a MWE. I'm just looking for a pat on the back.
> 
> https://lists.gnu.org/archive/html/lilypond-user/2024-05/msg00151.html
> 
> 
> Greetings to you all
> --
> Pierre-Luc Gauthier
> 
> P.S.: My nighttime reading is “git log -p” in the LilyPond repo. I’m
> always amazed by the incredibly competent work you guys do, year after
> year. I’m very grateful for all your hard work, advices, and support.
> <chordsInsideStaff.jpg>
> <LettreXL-basseElectrique.pdf>

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