It appears that you probably started the progress using version 1.0, then updated the game to version 1.0a, There were some significant file packing problems with the earlier version. So you will need to edit the save file to fix the differences. This is quite easy as the save file is plain text. Find all instances of ".gdc" and replace them with ".gd". Any decent text editor should have a replace function to accomplish this in an instant.
