### 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
const WindowData &wd = windows[p_window];
	
	Atom property = XInternAtom(x11_display, "WM_STATE", True);
	if (property == None) {
		return false;
	}
	Atom type;
	int format;
	unsigned long len;
	unsigned long remaining;
	unsigned char *data = nullptr;
	int result = XGetWindowProperty(
			x11_display,
			wd.x11_window,
			property,
			0,
			32,
			False,
			AnyPropertyType,
			&type,
			&format,
			&len,
			&remaining,
			&data);
	if (result == Success && data) {
		long *state = (long *)data;
		if (state[0] == WM_IconicState) {
			XFree(data);
			return true;
		}