Since 1.1 came out, I will have ships that will not be able to move to certain parts of the galaxy. If I move the ship one space, I will be able to move it to that area of the galaxy. I don't know wha the cause of the bug is, but what happens is when you right click on the destination, nothing will happen. You then need to right click on a destination close to the ship, then when it reaches that, go back and right click on the destination that you want it to go.
I'm not sure that I conveyed the problem very well, but if you need anymore information I will get thet for you when I get home.