When you choose an area with 'Rectangle Select' and then change the tool to 'Move Selection', and then move the selection using the arrow keys, when you crop the image using Ctrl + Alt + Z - the rectangle goes back to the position before you moved it with the arrows and then crops that area.
If you use the menu option 'Crop to Selection', there is no issue
If you move the box with the mouse, there is no issue.
The problem only occurs if you use the arrows key and the shortcut.
I have also noticed that when you use the menu option, and then undo, and then use the arrows key and shortcut ... the rectangle jumps back to where it was when you used the menu options - it seems like the box position isn't remember (and resets) when you use Ctrl+Alt+Z, but only when using the arrow keys to move the box.
Hope that makes sense.