### 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
0, 0, 
				0, 
				AnyPropertyType, 
				&type, 
				&format, 
				&len, &bytes_left, 
				&data);
		if (data) {
			XFree(data);
		}
		if (type == XInternAtom(x11_display, "INCR", 0)) {
			
			DEBUG_LOG_X11("INCR selection started.\n");
			LocalVector<uint8_t> incr_data;
			uint32_t data_size = 0;
			bool success = false;
			
			XDeleteProperty(x11_display, x11_window, type);
			
			bool done = false;
			while (!done) {
				if (!_wait_for_events()) {
					
					break;
				}
				
				XEvent ev;
				while (XCheckIfEvent(x11_display, &ev, _predicate_clipboard_incr, nullptr)) {
					result = XGetWindowProperty(x11_display, x11_window,
							selection,