/"$section"/ matches lines that contains a double quote followed by something that the regexp in $section matches followed by another double quote.

If you want to match lines that contain the text in $section, you want
/\Q$section\E/

If you want to match lines that are equal to the text in $section, you want
/^\Q$section\E\z/
or
$_ eq $section

I have no idea what's in $section, so it limits my ability to guess what you are trying to do and the advice I can give.

By the way, I noticed you changed
$_ .= $text;
to
$_ .= $_ .="$newline";
Why did you add quotes?

Thank you for the reply. It's now working a lot better than before. This now will add a line to the section of the file where I want it to, but it's adding $newline 2 lines under the $section string. I've included the section of code that calls this function. At this point I'm trying to track down if I have a problem with newline or returns because I'm mixing linux and windows environments when scripting and testing.

#Open add_lines.csv and add lines where needed
open(ADD, "$addstrings") || die("cannot open file $addstrings");
@addlines=<ADD>;
close(ADD);
foreach $line (@addlines)
{
    ($section,$newline)=split(/,<>,/,$line);
    chomp $section;
    chomp $newline;
    $newline = "\n".$newline;
    &AddLine($settings, $section, $newline);
}


sub AddLine{
my $file = $_[0];
my $section = $_[1];
my $newline = $_[2];
use Tie::File;
    tie @array, 'Tie::File', $file or die ("cannot open $file");
    print "Looking for section: $section so we can add line: $newline\
+n";    
    foreach (@array){        
        if (/\Q$section\E/){
        $_ .= $newline;
        last;
        }
    }
    untie @array;
[download]

I'm certain there is a better way to parse the CSV file but I'm not allowed to add perl modules in our setup.(otherwise I would use a excel parser module) I also had to consider possible string combinations in the values.

I see a lot of scoping errors (use "use strict" to reveal them). But that's not what you're asking about.

Actually, I don't know what you're asking about since you said "This now will add a line to the section of the file where I want it to".

By the way, I really don't see the point of using Tie::File here.