### 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
long left = struts[0];
								long right = struts[1];
								long top = struts[2];
								long bottom = struts[3];
								long left_start_y, left_end_y, right_start_y, right_end_y;
								long top_start_x, top_end_x, bottom_start_x, bottom_end_x;
								if (strut_len >= 12) {
									left_start_y = struts[4];
									left_end_y = struts[5];
									right_start_y = struts[6];
									right_end_y = struts[7];
									top_start_x = struts[8];
									top_end_x = struts[9];
									bottom_start_x = struts[10];
									bottom_end_x = struts[11];
								} else {
									left_start_y = 0;
									left_end_y = desktop_rect.size.y;
									right_start_y = 0;
									right_end_y = desktop_rect.size.y;
									top_start_x = 0;
									top_end_x = desktop_rect.size.x;
									bottom_start_x = 0;
									bottom_end_x = desktop_rect.size.x;
								}
								const Point2i &pos = desktop_rect.position;
								const Size2i &size = desktop_rect.size;
								Rect2i left_rect(pos.x, pos.y + left_start_y, left, left_end_y - left_start_y);
								if (left_rect.size.x > 0) {
									Rect2i intersection = rect.intersection(left_rect);