### Godot version

Master (0ddd9c3e8f9088fa139e25b2903289d727073e12)

### System information

PopOS 22.04 - Intel integrated graphics - all backends

### Issue description

When there are popup windows in the editor, I cannot click on the "Confirm"/"Cancel" type buttons at the button. 

I have the issue both in the project manager (importing projects I can click on files etc. but cannot click "open") and when running the editor (cannot click "Save&Quit" etc.)

Sometimes the editor correctly highlights the buttons and I can use the arrow keys to navigate the buttons and "enter" to confirm my selection.

_I can navigate the editor closing dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-24-06](https://user-images.githubusercontent.com/16521339/212774269-d784ea5e-5921-4460-9124-48978939c8e7.png)

_I can't navigate the project import dialogue with tab/arrow keys_
![Screenshot from 2023-01-16 14-29-00](https://user-images.githubusercontent.com/16521339/212774683-0a80795a-eed4-4e65-b2ca-3562c25d71fd.png)


### Steps to reproduce

Run the editor

### Minimal reproduction project

Reproducible in the project manager
gl_manager->window_destroy(E.key);
		}
#endif
		WindowData &wd = E.value;
		if (wd.xic) {
			XDestroyIC(wd.xic);
			wd.xic = nullptr;
		}
		XUnmapWindow(x11_display, wd.x11_window);
		XDestroyWindow(x11_display, wd.x11_window);
	}
	
#if defined(VULKAN_ENABLED)
	if (rendering_device_vulkan) {
		rendering_device_vulkan->finalize();
		memdelete(rendering_device_vulkan);
		rendering_device_vulkan = nullptr;
	}
	if (context_vulkan) {
		memdelete(context_vulkan);
		context_vulkan = nullptr;
	}
#endif
#ifdef GLES3_ENABLED
	if (gl_manager) {
		memdelete(gl_manager);
		gl_manager = nullptr;
	}
#endif
	if (xrandr_handle) {