The carriage returns aren't missing - PHP doesn't get hungry and start eating line breaks.
Instead, you're probably facing a different issue; you want line breaks in the data to result in line breaks in the text shown in your browser. Note that line breaks inside text in HTML markup is ignored by the browser; instead, you'll want to turn those line breaks into a <br> HTML entity. To that end, take a look at the function [man]nl2br/man.