This error is the most stupid thing i have seen i this tool, as if You have a flaw in defining a pad shape or padshape is not placed in the right folder or something like that, this error shows up.
Another resson could be You have a property called eg revision and it is a forth running number for having controll of Your footprints, and another person had the same property but as string..
When Your netlist is read only with warnings, then try place those giving the warning and read status in command window. This info is helpfull in many cases.