### 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
continue;
				}
				visualInfo = vi_list[i];
				if (pict_format->direct.alphaMask > 0) {
					break;
				}
			}
		}
		XFree(vi_list);
	}
	Colormap colormap = XCreateColormap(x11_display, RootWindow(x11_display, visualInfo.screen), visualInfo.visual, AllocNone);
	XSetWindowAttributes windowAttributes = {};
	windowAttributes.colormap = colormap;
	windowAttributes.background_pixel = 0xFFFFFFFF;
	windowAttributes.border_pixel = 0;
	windowAttributes.event_mask = KeyPressMask | KeyReleaseMask | StructureNotifyMask | ExposureMask;
	unsigned long valuemask = CWBorderPixel | CWColormap | CWEventMask;
	if (OS::get_singleton()->is_layered_allowed()) {
		windowAttributes.background_pixmap = None;
		windowAttributes.background_pixel = 0;
		windowAttributes.border_pixmap = None;
		valuemask |= CWBackPixel;
	}
	WindowID id = window_id_counter++;
	WindowData &wd = windows[id];
	if (p_flags & WINDOW_FLAG_NO_FOCUS_BIT) {
		wd.no_focus = true;
	}
	if (p_flags & WINDOW_FLAG_POPUP_BIT) {
		wd.is_popup = true;