Have you tried Tools -> Mesh -> Close Holes?
Is this the same problem you were having back here in June?: http://www.agisoft.com/forum/index.php?topic=3967.msg20557#msg20557Have you tried another PC, as it does seem like it's only you having the problem
You have the mesh open in a third party modeling program there? why not clean up the mesh manually then?
One last idea that comes to my mind is to try building (arbitrary) mesh with extrapolation (in advanced mesh settings). Not sure if it's going to change anything in your model. Have you updated PS recently?