### 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
XVisualInfo visualInfo;
	bool vi_selected = false;
#ifdef GLES3_ENABLED
	if (gl_manager) {
		visualInfo = gl_manager->get_vi(x11_display);
		vi_selected = true;
	}
#endif
	if (!vi_selected) {
		long visualMask = VisualScreenMask;
		int numberOfVisuals;
		XVisualInfo vInfoTemplate = {};
		vInfoTemplate.screen = DefaultScreen(x11_display);
		XVisualInfo *vi_list = XGetVisualInfo(x11_display, visualMask, &vInfoTemplate, &numberOfVisuals);
		ERR_FAIL_COND_V(!vi_list, INVALID_WINDOW_ID);
		visualInfo = vi_list[0];
		if (OS::get_singleton()->is_layered_allowed()) {
			for (int i = 0; i < numberOfVisuals; i++) {
				XRenderPictFormat *pict_format = XRenderFindVisualFormat(x11_display, vi_list[i].visual);
				if (!pict_format) {