I have tried both the 20070912 and 20080202 versions of PCB and found that most or all of the .pcb files open without any error messages. But unfortunately the components nor the traces can be seen. Only the inner planes can be seen. If I open a new file and place a component from our library everything looks good, so I don't think this is an issue with my computer not working with PCB properly (ie. a library display issue).
If I install the 20070208p1 release, which is what I had been using at UW, then the files appear normal and open properly.
It would be helpful to know what versions of PCB work with our layout files. It would also be useful to know how to migrate them forward assuming my above diagnosis is correct.
I am hypothesizing that there is something about the way we have configured the layers in our layout files that the new versions of PCB don't like.
I think this is actually a bug in PCB. I have quickly browsed the discussion list for PCB at sf.net and don't see this symptom discussed, however its possible they know about it. Its also possible its really my particular configuration.