What you are experiencing is the Windows Magnifier tool -- it's not actually a part of Screenshot Captor, but it can be launched from it, which is what you are doing.
By default this Windows Magnifier tool DOCKS to the top of your screen -- resulting in your windows shortcut icons being moved.
To solve this, move your mouse to the magnification window docked to your screen, and DRAG it off the top so that it no longer is docked but is instead floating somewhere. That should solve your problem.