That makes no sense. I have that exact build, and I get quotes: 
>c:\progs\perl588_817\bin\perl t.pl
"-leprint for @ARGV" -- -p blastn -d "value of $hu_seq value of $hd_se
+q" -i "value of $contig" -o "value of $alignment"

>c:\progs\perl588_817\bin\perl -v

This is perl, v5.8.8 built for MSWin32-x86-multi-thread
(with 25 registered patches, see perl -V for more detail)

Copyright 1987-2006, Larry Wall

Binary build 817 [257965] provided by ActiveState http://www.ActiveSta
+te.com
Built Mar 20 2006 17:54:25

Perl may be copied only under the terms of either the Artistic License
+ or the
GNU General Public License, which may be found in the Perl 5 source ki
+t.

Complete documentation for Perl, including FAQ lists, should be found 
+on
this system using "man perl" or "perldoc perl".  If you have access to
+ the
Internet, point your browser at http://www.perl.org/, the Perl Home Pa
+ge.

[download]

Maybe your echo is different. (Got cygwin?) Try switching echo for $^X: 

>c:\progs\perl588_817\bin\perl t.pl
-p
blastn
-d
value of $hu_seq value of $hd_seq
-i
value of $contig
-o
value of $alignment

[download]

In reply to Re^5: quoting issue with system command (Win32) by ikegami
in thread quoting issue with system command by lomSpace

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