Line-breaks in code blocks aren't parsed properly

When using a [code] block with line-breaks (the "\n" kind) they are firstly converted to <br /> tags and finally to <br />. The latter action is because there shouldn't be any working HTML tags inside code blocks, but it fails when parsing line-breaks. I've tried to find out where the problem lies myself, but I lack enough knowledge of the module and PHP to fix it. I guess it's got something to do with line 18 in bbcode-filter.inc, but whatever I edit, it doesn't change a thing.
$code_tag[1] = str_replace(array('<', '>'), array('&lt;', '&gt;'), $code_tag[1]);