To repro, first open this link on Apple.com showing Times Square. Notice how it displays where it should, horizontally centered in the frame.
Now open a Shockwave 3d piece in the same window (such as Xonko.com's Cooper Mini). Hurray! Using the latest version of Safari, that displays as it should as well.
Finally, return to Times Square, again in the same window, and the Quicktime VR content displays at an offset.
I have not been able to repro this with normal ('linear') quicktime movies, but all the Quicktime VR objects in the hardware gallery are broken, as are the panoramas at the World Wide Panorama project. Opening the movies in another window fixes the problem.
Update: sent in a bugreport