We also ran into this issue.
To reproduce it, try saving the contents of a textarea form field containing multiple lines of text to the database. If you then retrieve the field, and feed it into the replaceVariableByText() function with the parseLineBreaks option 'true', line breaks are not detected by phpdocx.
What "str_replace(array('\n\r', '\r\n', '\n', '\r'), '__LINEBREAK__', $value);" in the phpdocx source code does is look for the character '\', followed by 'r', followed by character '\', followed by 'n', or in hex notation: 5C 72 5C 6E, instead of 0D 0A.
It should work in the same fashion as the nl2br() php function.