@FordLawnmower I finally got to the bottom of this issue. I had hacked the JavaScript to remove the br's because I pass comments through a parser that calls nl2br. This was adding br's to each line of the code within comments, so I explicitly removed them from the code snippet. The side effect was it was also removing br's that should have been in the code. I came up with a solution to run nl2br on text outside the code tags. I wrote this function to solve it, http://www.hawkee.com/snippet/9705/