Your code is shown to work with this example. Please post an example that does not!

use strict;
use warnings;
use Data::Dumper;
my $inputFile = \do{
       "Omit this line \n"
    .  "Foo SEARCH Part 1 \n"
    .  "Part 2 \n"
    .  "Part 3 TEST bar \n"
    .  "Omit this line\n"
};

my $beginString = "SEARCH";
my $endString = "TEST";


my $fileContent;
open(my $fileHandler, '<', $inputFile) or die "Could not open file  $!
+";
{
    local $/;
    $fileContent = <$fileHandler>;
}
close($fileHandler);



if($fileContent =~ /\b$beginString\b(.*?)\b$endString\b/s){
    my $result = $1;
    print $result, "\n\n";
}

print Dumper($fileContent); 

OUTPUT:
 Part 1
Part 2
Part 3

$VAR1 = 'Omit this line
Foo SEARCH Part 1
Part 2
Part 3 TEST bar
Omit this line
';
[download]

Now do you understand "post an example"?