This function calls the native vbCompare() function in M$ Word and writes the output to a new Word doc. It dies on errors so wrap in an eval if you care.

sub CompareWord {
    my( $doc1, $doc2, $outfile) = @_;
    
    require Win32::OLE;
    $Win32::OLE::Warn = 3;    # die on errors...
    my $Word = Win32::OLE->GetActiveObject('Word.Application')
        || Win32::OLE->new('Word.Application', 'Quit');
    
    my $WordFile = $Word->Documents->Open($doc1);
    $Word->{Visible} = 0;
    $WordFile->Compare( $doc2 );
    $Word->WordBasic->FileSaveAs( $outfile);
    $WordFile->Close();
    
    undef $WordFile;
    undef $Word;
}