I an reproduce this on one of the sparkfun pro minis (the 5v one). When dragged to breadboard with grid size set at .1 in doesn't (and won't even if moved) align to the breadboard and connect. A work around is in View->Set grid size change the grid size from .1 to .01 and you can then drag the mini part til the connectors turn green (which indicates a connection to the breadboard). I should have pointed out in the post above that if you click on one of the mini connectors it should light up yellow. If the alignment to the breadboard is correct, the five breadboard connectors should also light up yellow (which I'd guess won't happen in your original). When the grid size is set to .01 and the mini snaps to the grid the mini pins go from red to green to indicate they have connected to the breadboard pins, and then the entire row goes yellow when clicked on. It looks to me as if the core parts may be not quite correctly aligned. I'll have a poke at that in a bit.
Peter