### 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
#include <sys/types.h>
#include <unistd.h>
#define WM_NormalState 1L  window normal state
#define WM_IconicState 3L  window minimized
#define _NET_WM_STATE_REMOVE 0L  remove/unset property
#define _NET_WM_STATE_ADD 1L  add/set property
#undef CursorShape
#include <X11/XKBlib.h>
#define XINPUT_CLIENT_VERSION_MAJOR 2
#define XINPUT_CLIENT_VERSION_MINOR 2
#define VALUATOR_ABSX 0
#define VALUATOR_ABSY 1
#define VALUATOR_PRESSURE 2
#define VALUATOR_TILTX 3
#define VALUATOR_TILTY 4
#ifdef DISPLAY_SERVER_X11_DEBUG_LOGS_ENABLED
#define DEBUG_LOG_X11(...) printf(__VA_ARGS__)
#else
#define DEBUG_LOG_X11(...)
#endif
static const double abs_resolution_mult = 10000.0;
static const double abs_resolution_range_mult = 10.0;
struct Hints {
	unsigned long flags = 0;
	unsigned long functions = 0;
	unsigned long decorations = 0;
	long inputMode = 0;
	unsigned long status = 0;
};
static String get_atom_name(Display *p_disp, Atom p_atom) {