That’s seems to be the window manager. It works with MATE.
Before asking I did only test xfce, Fluxbox and Gnome 
I tested on a laptop, with Debian 12 : with xfce it does it very rarely, but it does it sometimes.
It doesn’t seem to do it with MATE.
So maybe it does it very rarely with MATE too, if so I’ll tell here.
I’m on Debian 12, Linux 6.1.0-40-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.153-1 (2025-09-20) x86_64 GNU/Linux
I have a nVidia GeForce RTX4060, with the latest official driver, NVIDIA-Linux-x86_64-580.95.05
I tested to build the driver with the official modules and with the MIT/GPL, same results.
I use x11. I try to test with wayland but I haven’t still find how to activate it.
But the problem is here with Gnome on Xorg.
I repeat the problem :
When opening a plugin UI, first a window appears, and then the plugin UI appears,
and sometimes it’s not in the first window, like a component not well added. The first is then gliched. But the sizes always match.
Sometimes the two are glitched, sometimes there is only one. Even one time that crashed, when opening an UI (gxTuner, from Guitarix) :
AudioPluginHost: ../../../../src/cairo-error.c:68: _cairo_error: Assertion `_cairo_status_is_error (status)’ failed.
A few lines, diff of the results of xprop on each windows, but all seems normal.
$ diff with_UI_window other_window
0a1
> _NET_WM_ICON_GEOMETRY(CARDINAL) = 3900, 1034, 200, 23
2c3
< _NET_WM_ALLOWED_ACTIONS(ATOM) = _NET_WM_ACTION_CLOSE, _NET_WM_ACTION_ABOVE, _NET_WM_ACTION_BELOW, _NET_WM_ACTION_FULLSCREEN, _NET_WM_ACTION_MOVE, _NET_WM_ACTION_RESIZE, _NET_WM_ACTION_MAXIMIZE_HORZ, _NET_WM_ACTION_MAXIMIZE_VERT, _NET_WM_ACTION_CHANGE_DESKTOP, _NET_WM_ACTION_STICK
---
> _NET_WM_ALLOWED_ACTIONS(ATOM) = _NET_WM_ACTION_CLOSE, _NET_WM_ACTION_ABOVE, _NET_WM_ACTION_BELOW, _NET_WM_ACTION_FULLSCREEN, _NET_WM_ACTION_MOVE, _NET_WM_ACTION_RESIZE, _NET_WM_ACTION_MAXIMIZE_HORZ, _NET_WM_ACTION_MAXIMIZE_VERT, _NET_WM_ACTION_MINIMIZE, _NET_WM_ACTION_CHANGE_DESKTOP, _NET_WM_ACTION_STICK
6a8
> _NET_WM_STATE(ATOM) =
8,11c10,13
< user specified location: 0, 0
< user specified size: 1 by 1
< WM_ICON_NAME(UTF8_STRING) =
< WM_NAME(UTF8_STRING) =
---
> user specified location: 235, 96
> user specified size: 450 by 343
> WM_ICON_NAME(UTF8_STRING) = "ZamTube (LV2)"
> WM_NAME(UTF8_STRING) = "ZamTube (LV2)"
20d21
< _NET_WM_STATE(ATOM) = _NET_WM_STATE_SKIP_TASKBAR
Thanks for the answer. And sorry, my question missed details indeed.