I encountered this problem with the following situation: I opened documents that were created in Quark 3.x, subsequently saved as Quark 4.x and/or Quark 5.x. I automatically did a collect for output and when prompted to save the file, I did so first. V 6.x was my only option for this. I then finished the collect for output. After it was done, and the file refreshed itself, all the text on the second page was lost as well as some graphics on first page (only a 2 page document).
I can recreate it again and again in the same circumstances, but I cannot duplicate any other time. Saved as Quark 6.x, thumbnail drag from Quark 5.x and then opened and saved in Quark 6.x, subsequently collecting for output or anything. All seems to work... except the situation described above... I will post back with any other problems found.