I can not see coments 2,3, or 5, so far. I hope they helped you with this issue and you can see them. You can add #s 7 and 9 as well for me.
Spyhunter1337
I don't know if you have figured this out yet but in case not I Had the same problem and it took me a week to get it fixed. the problem was just like what you describe but I noticed that my bootskin upon loading was a little off center as well and all the tweaking in the world did nothing to fix it, I finally saved the skin as a different format .jpg to be exact I had to convert it to RGB first, and opened the new file up and went from square one like
I think its really good, one thing though in the part about making selections of a given size. When you are using the tool look up at the tool bar where the tool options are and you will see a drop down box (probably says normal) that lets you set it to a fixed size. and then just click there's your box, now if you click inside the box with the tool you can drag it around or you can move it with the arrow keys. You can nudge one pixel at a time by tapp