### 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
static unsigned char all_master_mask_data[XIMaskLen(XI_LASTEVENT)] = {};
		all_master_event_mask.deviceid = XIAllMasterDevices;
		all_master_event_mask.mask_len = sizeof(all_master_mask_data);
		all_master_event_mask.mask = all_master_mask_data;
		XISetMask(all_master_event_mask.mask, XI_DeviceChanged);
		XISetMask(all_master_event_mask.mask, XI_RawMotion);
		XISelectEvents(x11_display, DefaultRootWindow(x11_display), &all_master_event_mask, 1);
	}
	cursor_size = XcursorGetDefaultSize(x11_display);
	cursor_theme = XcursorGetTheme(x11_display);
	if (!cursor_theme) {
		print_verbose("XcursorGetTheme could not get cursor theme");
		cursor_theme = "default";
	}
	for (int i = 0; i < CURSOR_MAX; i++) {
		static const char *cursor_file[] = {
			"left_ptr",
			"xterm",
			"hand2",
			"cross",
			"watch",
			"left_ptr_watch",
			"fleur",
			"dnd-move",
			"crossed_circle",
			"v_double_arrow",
			"h_double_arrow",
			"size_bdiag",
			"size_fdiag",
			"move",