### 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
if (do_mouse_warp) {
		XWarpPointer(x11_display, None, windows[MAIN_WINDOW_ID].x11_window,
				0, 0, 0, 0, (int)windows[MAIN_WINDOW_ID].size.width / 2, (int)windows[MAIN_WINDOW_ID].size.height / 2);
		/*
		Window root, child;
		int root_x, root_y;
		int win_x, win_y;
		unsigned int mask;
		XQueryPointer( x11_display, x11_window, &root, &child, &root_x, &root_y, &win_x, &win_y, &mask );
		printf("Root: %d,%d\n", root_x, root_y);
		printf("Win: %d,%d\n", win_x, win_y);
		*/
	}
	Input::get_singleton()->flush_buffered_events();
}
void DisplayServerX11::release_rendering_thread() {
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		gl_manager->release_current();
	}
#endif
}
void DisplayServerX11::make_rendering_thread() {
#if defined(GLES3_ENABLED)
	if (gl_manager) {
		gl_manager->make_current();
	}
#endif
}
void DisplayServerX11::swap_buffers() {