Okay...
1. It's normal for "Add" to give Object 0; that's basically the filler until you change it. The "From Selection" button actually sets the selected entry to the window you have selected. Nonetheless, I made a couple of improvements here - firstly, when clicking "Add" the new addition is automatically selected, and secondly, if the user has a single window selected, it'll set the new entry to that.
2. I have no idea what you mean by this, could you explain please?
3. This will occur if any entry in the window order list refers to an object beyond the last object in the level. I'll make a change to the editor so it won't save such entries.