Almost every academic conference and journal that I’ve submitted my work to has required that a different style to be applied to my paper. This is less trouble than it might sound, since I use LaTeX to typeset my documents, and it does most of the work for me.
The exception to this rule, however, is the Web conference, which requires an XHTML version of the paper in addition to the PDF, and by XHTML I mean a version that adheres to their particular use of element class names (for linked CSS stylesheets) and is valid XML. Unfortunately, no existing LaTeX to HTML converter does the job, so I’ve had to do it by hand.
It was exactly the same last year, although I didn’t miss the pub that time as a result 🙁