I have encountered a problem with the autonauts robots command order being screwed up every time I lose focus in full-screen. What I do is I either alt-tab or press the windows key to hide it away, but when I come back to the game, the robots are always on the wrong step of a command line.

I then changed the focus to look at your posting. Because I always use "windowed mode" in Autonauts, I could still see the steps that the bot followed while the focus had changed, as shown below.
Although the bot some times needed to wait at the "Find nearest Dung" step until a cow had dumped a dung, it would continue to follow all of the step as long as there was room in the Compost Bin. When there was no room in the Compost Bin, the bot couldn't add the dung and so it would fail several steps. Perhaps that might be similar to what happened with your bot. Since you said "Trying to pick stuff up with a hand that should be empty", maybe you were implying that there was a failure when the hands were not empty. If so, I can understand that the bot would fail there. I would view that as an opportunity to try to find a solution (perhaps using a "Repeat 1 times" loop with the test-for-failure option checked).