### 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
int _group_count = 0;
	XkbDescRec *kbd = XkbAllocKeyboard();
	if (kbd) {
		kbd->dpy = x11_display;
		XkbGetControls(x11_display, XkbAllControlsMask, kbd);
		XkbGetNames(x11_display, XkbSymbolsNameMask, kbd);
		const Atom *groups = kbd->names->groups;
		if (kbd->ctrls != nullptr) {
			_group_count = kbd->ctrls->num_groups;
		} else {
			while (_group_count < XkbNumKbdGroups && groups[_group_count] != None) {
				_group_count++;
			}
		}
		XkbFreeKeyboard(kbd, 0, true);
	}
	return _group_count;
}
int DisplayServerX11::keyboard_get_current_layout() const {
	XkbStateRec state;
	XkbGetState(x11_display, XkbUseCoreKbd, &state);
	return state.group;
}
void DisplayServerX11::keyboard_set_current_layout(int p_index) {
	ERR_FAIL_INDEX(p_index, keyboard_get_layout_count());
	XkbLockGroup(x11_display, XkbUseCoreKbd, p_index);
}
String DisplayServerX11::keyboard_get_layout_language(int p_index) const {