I have initialised tinyMCE like so:
$(\'#description\').tinymce({
// Location of TinyMCE script
script_url : \'tinymce/jscripts/tiny_
In case anyone comes across this in the future, we were having issues with linebreaks being stripped and tried just about every suggestion we could find, with no luck.
I came across this solution here: http://community.tinymce.com/forum/viewtopic.php?id=5636, and it did the trick perfectly.
Add the following two lines two the tinyMCE.init() function, by default they seem to be set to false.
force_p_newlines : true,
force_br_newlines : true