Odd, I have Cygwin installed, permitting access to lsand grepcommands. This works fine on my system:

#!/usr/bin/perl

use strict;

{
    my @ret1 = `ls`;
    print "[@ret1]\n";

    my @ret2 = `ls | sort -r`;
    print "[@ret2]\n";
}

exit;

__END__

C:\Steve\Dev\PerlMonks\P-2013-10-24@0940-BackTick-Pipe>testbacktick.pl
[test1.dat
 test2.dat
 test3.dat
 testbacktick.pl
]
[testbacktick.pl
 test3.dat
 test2.dat
 test1.dat
]
[download]

Added: Could it be that psexecmight be messing with your command string? Maybe you can pre-escape the pipes with backslashes or somesuch?