Ckeditor inserting html <br> at new line

Hi .. I'm using ckeditor with Wordpress with a self-written plugin that builds html tables from a load of shortcodes. This is all working well apart from the fact that each as shortcode is entered on a new line, the line breaks are being converted into html <br> tags which then messes up the table.

Is there an easy way to stop this happening please ? I've tried configuring ckeditor but I can't find a way to stop this behaviour(which is probably natural if the editor has to convert text into HTML). I don't necessarily want to change the editor behaviour completely as the conversion may be required for other pages. Would be good to have sort sort of escape tags so that no conversions are done between an escape and a corresponding end tag.

Thanks

Ron