bplegend,
I assume that you pull the array in from somewhere else rather than as you put it in your code snippet
That is, when I tried your code above after adding warnings and strict. Perl complained that I was using a bareword because the "\'" after the c is translated as an escaped "'" and not the end of the variable.
Have you checked for any errors coming up?
It seems to work fine for me.
I tried;

#!/usr/bin/perl -w
use strict;
my @row;
my $separator=',';
open(INPUT,"< temp.txt") or die "could not open";
while(<INPUT>){ chomp; push @row,$_;};
foreach (@row) {
  s/(\\+)/$1$1/g;
}
print join($separator, @row);
print "\n";
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and got aa,bb,\\\\c\\c\\,d\\d
temp.txt contained

aa
bb
\\c\c\
d\d
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