I really don't know what this term means, to be frank, but common sense would suggest that "real" means that the course is actually currently taught, or is currently available to be taken by a given student or group of students, as opposed to courses that are "on the books" but not actually available for some reason. There is hardly anything on this on the Internet, as I'm sure you've found too.

"Las diferencias según sexo en la elección de optativas reales que se cursan actualmente en la Región de Murcia"
http://books.google.es/books?id=FpSpxsMjlecC&pg=PA228&lpg=PA...

Here I would guess that "actualmente" means that the optativas reales are those currently taught.

"*Las optativas de francés y alemán solo se ofrecen a quienes hayan cursado dicho idioma a lo largo de la carrera. Por este motivo se indica que se ofrecen 10 optativas reales para cada alumno aunque en total se ofrezcan 11."
http://www.uva.es/export/sites/default/portal/adjuntos/docum...

Here there is a list of 11 subjects but only 10 of them at most are available to any given student.