This is the kind of thing I experience whenever my zero-registration in the component footprint is off by a lot. It looks like your components have a large difference from the Y-zero-point to the actual pad.
Try opening the footprint editor, press E for Edit, F for Set Reference, and choose Pin 1, Center or Location.
Pin 1 sets the origin in the center of your Pin 1 (obviously), Center sets the origin in the center of your component horizontally and vertically and Location lets you select an origin at any point on your grid.
Oh, and after doing this, delete the components from your layout and do another "Update PCB Document" to reimport the components to good default locations.