### 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
Window root_return, child_return;
	int root_x, root_y, win_x, win_y;
	unsigned int mask_return;
	Bool xquerypointer_result = XQueryPointer(x11_display, wd.x11_window, &root_return, &child_return, &root_x, &root_y,
			&win_x, &win_y, &mask_return);
	if (xquerypointer_result) {
		if (win_x > 0 && win_y > 0 && win_x <= wd.size.width && win_y <= wd.size.height) {
			last_mouse_pos.x = win_x;
			last_mouse_pos.y = win_y;
			last_mouse_pos_valid = true;
			Input::get_singleton()->set_mouse_position(last_mouse_pos);
		}
	}
}
bool DisplayServerX11::_refresh_device_info() {
	int event_base, error_base;
	print_verbose("XInput: Refreshing devices.");
	if (!XQueryExtension(x11_display, "XInputExtension", &xi.opcode, &event_base, &error_base)) {
		print_verbose("XInput extension not available. Please upgrade your distribution.");
		return false;
	}
	int xi_major_query = XINPUT_CLIENT_VERSION_MAJOR;
	int xi_minor_query = XINPUT_CLIENT_VERSION_MINOR;
	if (XIQueryVersion(x11_display, &xi_major_query, &xi_minor_query) != Success) {
		print_verbose(vformat("XInput 2 not available (server supports %d.%d).", xi_major_query, xi_minor_query));
		xi.opcode = 0;
		return false;
	}
	if (xi_major_query < XINPUT_CLIENT_VERSION_MAJOR || (xi_major_query == XINPUT_CLIENT_VERSION_MAJOR && xi_minor_query < XINPUT_CLIENT_VERSION_MINOR)) {