### 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
r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load Xinerama dynamically.");
	}
	if (initialize_xrandr(dylibloader_verbose) != 0) {
		r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load Xrandr dynamically.");
	}
	if (initialize_xrender(dylibloader_verbose) != 0) {
		r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load Xrender dynamically.");
	}
	if (initialize_xinput2(dylibloader_verbose) != 0) {
		r_error = ERR_UNAVAILABLE;
		ERR_FAIL_MSG("Can't load Xinput2 dynamically.");
	}
	Input::get_singleton()->set_event_dispatch_function(_dispatch_input_events);
	r_error = OK;
	for (int i = 0; i < CURSOR_MAX; i++) {
		cursors[i] = None;
		img[i] = nullptr;
	}
	XInitThreads(); 
	
	x11_display = XOpenDisplay(nullptr);
	if (!x11_display) {
		ERR_PRINT("X11 Display is not available");
		r_error = ERR_UNAVAILABLE;
		return;
	}
	char *modifiers = nullptr;