Interestingly, when I run your snippet with an ActivePerl 5.8.8, I get the undesirable behavior (no quoting) you report with 5.6.0: 

c:\>perl t.pl
-leprint for @ARGV -- -p blastn -d value of $hu_seq value of $hd_seq -
+i value of $contig -o value of $alignment

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So there seems to be more to it than just version > 5.6.0 (?)

In order to keep, lets say, 'value of $alignment' together as one argument, I have to define an ugly my $alignment = '\"value of $alignment\"';. 

c:\>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

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In reply to Re^4: quoting issue with system command (Win32) by almut
in thread quoting issue with system command by lomSpace

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