### 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_
#ifdef DISPLAY_SERVER_X11_DEBUG_LOGS_ENABLED
	static int frame = 0;
	++frame;
#endif
	bool ignore_events = mouse_process_popups();
	if (app_focused) {
		
		bool focus_found = false;
		for (const KeyValue<WindowID, WindowData> &E : windows) {
			if (E.value.focused) {
				focus_found = true;
				break;
			}
		}
		if (!focus_found) {
			uint64_t delta = OS::get_singleton()->get_ticks_msec() - time_since_no_focus;