Double encoding of carriage returns in scripts

When trying to use scripts in edit source (text/html) I end up with double encoded characters for carriage returns (
). I've got it to the point where as long as the js command is a one liner it runs thanks to the documentation. However as soon as it has CRs in there for readability it substitutes all of them for that encoding. Changing the tinyMCE entity_encoding doesn't have an effect (Assuming I'm using it right. Compiling then restarting). If any of you have experience using scripts in the included editor your insight would be welcome!