I had the same problem with a similar skin.
Notice that in your first picture, your "white" boxes where the programs are listed are in line with each other. In the second picture you can tell that you adjusted the wrong settings because those white areas are not in line anymore.
So, once you have changed that to the original, do the following:
Change your "Places" (i.e. dark region) margins. More specifically, you need to change the "text" or "content" margins for the "Places" box so that on the left side you have a more positive value. Do a noticeable change of 20 pixels or so and see how that affects it. I hope that does it for you.