Any chance that the file got saved by Visio 2002, which can also write the
same file format? You may be carrying around a bunch of unused shapes. One
thing to check is the Document Stencil. Go to File > Stencils > Show
Document Stencil. Select a master shape and try to delete it. If you
succeed, then that shape was not being used and just taking up space. If
you get a warning, then cancel since the shape is in use.