I noticed a similar issue when using Getopt::Long. Regardless of whether it's a problem with the shell or not, quoted strings don't get through intact. I wrote a simple function that takes a command line and splits it into @ARGV. You could probably modify it to work on the already-split @ARGV directly, or just do this first:

$cmdline = join(' ',@ARGV);
parsetoargv($cmdline);
[download]

Here's the function:

sub parsetoargv {
  my ($cmdline, $idx) = (shift, 0);

  @ARGV = ();

  {
    $cmdline =~ m{ \G\               }gcx && do {redo}; # Eat a space

    $cmdline =~ m{ \G"               }gcx && do {       # Start a quot
+ed-string
      $cmdline =~ m{ \G(.*?)(?<!\\)" }gcx && do {       #   Match up t
+o the next unescaped quote
        ($ARGV[$idx++] = $1) =~ s/\\"/"/g;              #     And put 
+it in ARGV, removing escaping slashes
      }; redo
    };

    $cmdline =~ m{ \G(.*?)(?="|\ |$) }gcx && do {       # Match up to 
+just before the next quote, space, or end-of-line
      $ARGV[$idx++] = $1 if ($1 ne ''); redo            #  And put it 
+in ARGV if it isn't empty
    };
  }
}
[download]

Now your @ARGV is ready for GetOptions.