AFAIK there is no metadata in an mbox file that determines if a particular message has been read or not? Please correct me if I am wrong.

The first thing I did was to run the podchecker program on yours and it produced two syntax errors.

Some comments:

    159 sub wanted
    160 {
    161     my $file = $File::Find::name;
    162 
    163     #
    164     # We only care about files.
    165     #
    166     return if ( -d $file );
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I guess you are assuming that there are no named pipes or FIFOs or other types of files?

    167 
    168     #
    169     # Skip some mailboxes.
    170     #
    171     foreach my $exclude ( split( /,/, $CONFIG{'exclude'} ) )
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What if you have a file name with a comma in it?

    172     {
    173         if ( $file =~ /$exclude/i )
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What if you have a file name with a regex meta-character in it? What if the contents of $exclude are a subset of a larger file name? $file includes the complete path so $exclude could match on one of the path names. What if you want to exclude 'file' but not 'FILE'?

    174         {
    175             $CONFIG{'verbose'} && print "Excluded mail file: $
+file\n";
    176             return;
    177         }
    178     }
    179 
    180 
    181     #
    182     #  Skip files if they've not been modified too recently.
    183     #
    184     my $time = -M $file;
    185     if ( defined( $time ) )
    186     {
    187         if ( $time > $CONFIG{'time'} )
    188         {
    189             $CONFIG{'verbose'} && print "Mail file not modifie
+d recently: $file\n";
    190             return;
    191         }
    192     }
    193     else
    194     {
    195         $CONFIG{'verbose'} && print "Failed to stat: $file - $
+!\n";
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You report an error if you cannot stat the file but not at line 166?

    196         return;
    197     }
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HTH

Edit: g0n - moved comments out of code tags