Hey, the same problem just happen to me; everything was working fine and then before I knew it, the scale manipulators disappeared. I'm sometimes confused between the many shortcuts I use for other programs and hit random keys when I'm modeling in maya, which leads me to: what bloody key have I hit to cause that??
I haven't worked at all on my prefs so I deleted the file and everything went back to normal... is there a way to have a log of all the keys you pressed in a session?