A few more things.
First, I restarted and since then I haven't been able to reproduce the z order not changing on first click thing. Maybe that was just a glitch?
Second, I accidentally pressed control r (which I'm guessing is reset?) rather then control y when I wanted to do a redo. After the reset I wasn't about to use control z or anything to get the project back. Maybe do an autosave before completing the reset or a confirm reset dialogue or something?
Third, have you added the option to add the black outline around the sets of parts like you did in that robot post a while back?