It is the loss of the line breaks which is the biggest annoyance. That will cause significant problems for newcomers who are trying to copy and paste code into their own pages. Not user-friendly!
As you say, it dos not happen with php tags, so why does it happen with Javascript code tags? It must be a coding error. Please fix it soon - whoever did it managed to introduce this glitch into the forum up within hours, so why can he not put it right in hours?