Given it's 100% reproducible on my build, I went ahead with some testing of configuration options.

It seems related to PGTK. ./configure --with-pgtk has the bug whereas the version without it does not. Given the warning message about using PGTK with X11, I assume that this falls under the same umbrella, and that I should go complain to the package builders.

Let me know if there's anything more to look at.
Patrick

On Sun, May 28, 2023 at 1:23 AM Eli Zaretskii <eliz@gnu.org> wrote:
> From: Patrick Poitras <patrick.f.poitras@gmail.com>
> Date: Sat, 27 May 2023 22:16:31 -0700
>
> Start emacs with `emacs -Q`
>
> M-x pixel-scroll-precision-mode
>
> Scroll a large buffer, works great.
>
> Click and drag to select a region in the buffer. Click somewhere else in the buffer. to unselect it.
> Scrolling around will now randomly skip entire pages after scrolling 4-5 lines. This makes the mode
> unusable.

I cannot reproduce this, FWIW.  The effect of scrolling is the same
before and after selecting a region.

Perhaps this is one more effect of known (and not yet solved) issues
with native-compilation?  My Emacs was build without it.