### 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
_THREAD_SAFE_METHOD_
	switch (p_screen) {
		case SCREEN_PRIMARY: {
			p_screen = get_primary_screen();
		} break;
		case SCREEN_OF_MAIN_WINDOW: {
			p_screen = window_get_current_screen(MAIN_WINDOW_ID);
		} break;
		default:
			break;
	}
	
	ERR_FAIL_INDEX_V(p_screen, get_screen_count(), SCREEN_REFRESH_RATE_FALLBACK);
	
	if (xrandr_ext_ok) {
		XRRScreenResources *screen_info = XRRGetScreenResources(x11_display, windows[MAIN_WINDOW_ID].x11_window);
		if (screen_info) {
			RRMode current_mode = 0;
			xrr_monitor_info *monitors = nullptr;
			if (xrr_get_monitors) {
				int count = 0;
				monitors = xrr_get_monitors(x11_display, windows[MAIN_WINDOW_ID].x11_window, true, &count);
				ERR_FAIL_INDEX_V(p_screen, count, SCREEN_REFRESH_RATE_FALLBACK);
			} else {
				ERR_PRINT("An error occurred while trying to get the screen refresh rate.");
				return SCREEN_REFRESH_RATE_FALLBACK;
			}
			bool found_active_mode = false;
			for (int crtc = 0; crtc < screen_info->ncrtc; crtc++) { 
				XRRCrtcInfo *monitor_info = XRRGetCrtcInfo(x11_display, screen_info, screen_info->crtcs[crtc]);