Russ,
I don't think you have the same setup. Notice how your larger physical display (Thunderbolt) has the white banner (menu bar). Mine is reversed as the laptop display is primary.
Juan, if I swap the menu bar (white banner) as shown in the screenshot Russ uploaded, by dragging that white banner to the physically larger display (Thunderbolt) the logo issue is resolved for both application start and the acknowledgements. Once that's done, it doesn't matter whether the monitor arrangement is side-by-side or top-to-bottom.
Could it have something to do with the Retina display being primary (menu bar) @ 2880 x 1800 and the Thunderbolt display being limited to 2560 x 1440?
At any rate, glad we got to the bottom of this for you. Try moving your menu bar to the laptop/smaller display and see if you can reproduce my cropped start up logo and/or acknowledgements dialog.
Bottom line is if the Retina display is Primary (has the white menu bar) the startup logo and acknowledgement screens will be cropped. If your external display of lower resolution is Primary, the logos will appear normal.