Shader editing window issues, vanishing boxes and blinking windows

### Tested versions

was having issues with it in 4.3 and thought maybe updating to 4.4 would fix, it did not

### System information

Godot v4.4.dev7 - Windows 10 (build 19044) - Multi-window, 1 monitor - OpenGL 3 (Compatibility) - Intel(R) HD Graphics 620 (Intel Corporation; 24.20.100.6025) - Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz (4 threads)

### Issue description

Godot v4.4.dev7 - Windows 10 (build 19044) - Multi-window, 1 monitor - OpenGL 3 (Compatibility) - Intel(R) HD Graphics 620 (Intel Corporation; 24.20.100.6025) - Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz (4 threads)

### Steps to reproduce

I am new to this so please be patient with my lack of CS lingo
-gpu particles 3d node
-process material -new particle process material
-drawpass prism mesh
-accelerations gravity -0.1
-set to single particle
-geometry new shader material
-shader: new shader
-visual shader
-flags enable unshaded
-new node on shader edit, particle color
-connect particle color to albedo

result:

### Minimal reproduction project (MRP)

I tried to reproduce this in a fresh project following identical steps, and it didn't recreate. The project included doesn't have many files in it, but I don't know which ones are causing the issue. I am sorry if i did something wrong in the bug reporting process

[bug.zip](https://github.com/user-attachments/files/18209496/bug.zip)

Start with the attached bug.zip and follow the listed GPU-particles and visual-shader steps in Godot v4.4.dev7 on Windows 10 with OpenGL 3. The fresh-project attempt did not reproduce the problem, so first isolate the project or environment conditions that cause the shader editing boxes to vanish and windows to blink; done means reproducing and fixing the behavior with a regression check.

Written by the indexing model from the issue text.