### 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
if (p_target == XInternAtom(x11_display, "TARGETS", 0)) {
		
		Atom data[9];
		data[0] = XInternAtom(x11_display, "TARGETS", 0);
		data[1] = XInternAtom(x11_display, "SAVE_TARGETS", 0);
		data[2] = XInternAtom(x11_display, "MULTIPLE", 0);
		data[3] = XInternAtom(x11_display, "UTF8_STRING", 0);
		data[4] = XInternAtom(x11_display, "COMPOUND_TEXT", 0);
		data[5] = XInternAtom(x11_display, "TEXT", 0);
		data[6] = XA_STRING;
		data[7] = XInternAtom(x11_display, "text/plain;charset=utf-8", 0);
		data[8] = XInternAtom(x11_display, "text/plain", 0);
		XChangeProperty(x11_display,
				p_requestor,
				p_property,
				XA_ATOM,
				32,
				PropModeReplace,
				(unsigned char *)&data,
				sizeof(data) / sizeof(data[0]));
		return p_property;
	} else if (p_target == XInternAtom(x11_display, "SAVE_TARGETS", 0)) {
		
		XChangeProperty(x11_display,
				p_requestor,
				p_property,
				XInternAtom(x11_display, "NULL", False),
				32,
				PropModeReplace,