I think, just having a look at it, it's alphabetically by _filename_, not by the name of the map itself. Thus "The Desert Eye", which has the filename eye.map, will be ordered under E. However, despite ordering by filename alphabetically, the game displays by map name. The title of the map displayed in the game is just in the .map file:
Quote:
-- Title and image file
#dom2title The Desert Eye
#imagefile eye.tga
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Well, that's what I found, I am running the demo though. I have played around with lots of other maps though, downloaded and randomly created myself. My full Version's in the post 
.