First of all you should improve your error handling. Checking -e after a failed open is prone to race conditions, and there are other reasons why an open could fail. Try something along these lines:

my $isOpen = open($handle, $templateLocation); 
if (!$isOpen) {
    my $exception = MidTier::Exception->new("2",
            "Error opening file `$templateLocation' for reading: $!", 
+$self);
    # no need to close never opened handles
    $exception->sendLog();
    die; # unless $exception->sendlog() dies anyway
} 

$logger->debug("File $templateLocation opened");
$logger->info("Building template: $template");
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Then note that if (!$line test dangerous - what if a line is a false value for perl? (ie a 0 without a newline after it).

(Another stupid idea from me: maybe the template file just lives on a network file system, and the connection hangs, and that's why you're getting timeouts?)