#!/usr/bin/perl -w
use strict;

my @a = ( "asdfadsf  df\n", 
         "qrwtqtre ab\n");
my $ref = \@a;

print "simple print\n";
foreach my $line (@a)
{
   print $line;
}

print "\nnow with chomp\n";
foreach my $line (@$ref)
{
    chomp $line; ## this modifies @a
    print "$line**";
}

print "\nnow again simple print\n";
foreach my $line (@a)
{
   print $line;
}

__END__
simple print
asdfadsf  df
qrwtqtre ab

now with chomp
asdfadsf  df**qrwtqtre ab**
now again simple print
asdfadsf  dfqrwtqtre ab
[download]

looks like it works, maybe there is some other piece of code that isn't shown? perhaps try s/\s*$//; to get rid of ALL white space at the end of line.