(Note that one major difference is that the June plan is in color and the September plan is not; I'm not sure if that's an artifact of the scan I received from the ESDC yesterday or not. Click on graphics to enlarge.)
The June site plan
Note that this plan, dated 9/4/08, is attributed to Gehry Architects and contains adjacent streets and landmarks. It references a hotel, street-level retail, and a bicycle station.
The September site plan
This plan, though containing most of Gehry's building layout, does not mention retail (surely a street-level factor). Nor does it mention a hotel (now unlikely) or a bicycle station (likely part of the plan, though it may have been moved). There's no name or date on the plan.