### 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
XFreeEventData(x11_display, &event.xcookie);
			continue;
		}
		WindowID window_id = MAIN_WINDOW_ID;
		
		for (const KeyValue<WindowID, WindowData> &E : windows) {
			if (event.xany.window == E.value.x11_window) {
				window_id = E.key;
				break;
			}
		}
		if (XGetEventData(x11_display, &event.xcookie)) {
			if (event.xcookie.type == GenericEvent && event.xcookie.extension == xi.opcode) {
				XIDeviceEvent *event_data = (XIDeviceEvent *)event.xcookie.data;
				int index = event_data->detail;
				Vector2 pos = Vector2(event_data->event_x, event_data->event_y);
				switch (event_data->evtype) {
					case XI_HierarchyChanged:
					case XI_DeviceChanged: {
						_refresh_device_info();
					} break;
					case XI_RawMotion: {
						XIRawEvent *raw_event = (XIRawEvent *)event_data;
						int device_id = raw_event->sourceid;
						
						
						
						if (raw_event->valuators.mask_len <= 0) {
							break;
						}