Great question. In order for FAB 3000 to automatically add components, FAB 3000 needs to know what your selected gerber pads looks like at 0 degrees (no rotation). Once FAB 3000 knows what the footprint looks like at zero, it can scan your Gerber files and apply the correct rotation.
The graphic window is only used as a guideline to give you a "visual confirmation" that your part is correctly orientated (at zero). If you do not see the gerber pads correctly orientated at zero (only in the dialog), you will need to select the "rotation" control until it appears orientated as zero.
For example think of anytime you review a component data sheet from a component manufacturer (like Samsung, etc.). It always shows the component footprints orientated at 0 degrees on that data sheet, even though on your board that component will be most likely rotated at another angle besides 0. Knowing what the component looks like at 0 degrees rotation, makes it easier for FAB 3000 to scan and detect what angle to use when adding components to your PCB.
Hope that helps.