My apologies for not being more clear, Ariel,
Unfortunately, that viewer only accepts individual Deep Zoom Images (.dzi), rather than Deep Zoom Collections (.dzc). When viewing the DZC's xml in your browser, you should be able to see the URLs of each DZI inside and copy any one of them to paste into the viewer.
Viewing the images, one at a time, in another viewer is, I suppose, not all that practical, except to confirm that there really is part of the image missing or out of interest for seeing that the image is viewable other places other than within the Photosynth viewer.
Another interesting experiment would be to collect the URLs of the DZIs from both version 3 and version 5 of your synth, paste them both into Excel in different colours, and then sort both lists as one alphabetically to see whether the latter version is reusing any of the same DZIs that previous versions stored on the server. I expect them to all be different, since you tagged them in between.