I know this is a very old post and most likely you've long forgotten it. However, I wanted to chime in just in case someone else experiences this.
I just experienced this in Moodle 3.0 and discovered that it was caused by an instructor entering a calculation formula for the Course Total. Once that calculation was removed, the aggregation drop-down menu re-appeared and all was well again with the world! I tested this on other categories, other than just the course total, and the same thing happened.