### 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
wd.position.x = xwa.x;
		wd.position.y = xwa.y;
		wd.size.width = xwa.width;
		wd.size.height = xwa.height;
	}
	
	if (cursors[current_cursor] != None) {
		XDefineCursor(x11_display, wd.x11_window, cursors[current_cursor]);
	}
	return id;
}
DisplayServerX11::DisplayServerX11(const String &p_rendering_driver, WindowMode p_mode, VSyncMode p_vsync_mode, uint32_t p_flags, const Vector2i *p_position, const Vector2i &p_resolution, int p_screen, Error &r_error) {
#ifdef DEBUG_ENABLED
	int dylibloader_verbose = 1;
#else
	int dylibloader_verbose = 0;
#endif
	if (initialize_xlib(dylibloader_verbose) != 0) {
		r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load Xlib dynamically.");
	}
	if (initialize_xcursor(dylibloader_verbose) != 0) {
		r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load XCursor dynamically.");
	}
	if (initialize_xext(dylibloader_verbose) != 0) {
		r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load Xext dynamically.");
	}
	if (initialize_xinerama(dylibloader_verbose) != 0) {