Julie,
 
When deciding on my graduate course of study, I found a book called Museums: A Place to Work, Planning Museum Careers.  It is by Jane R. Glaser with Artemis A. Zenetou.  I got it from the AAM bookstore (online at the website).   Chapter 8 discusses "Training and preparation" and states: "Many of the best programs offer master's degrees in a discipline with a certificate in Museum Studies."  Later in the chapter the author(s) state that "Programs (Museum Studies) may be oriented toward history, the sciences, anthropology or art, for example, or they may have important strengths in such work areas as curatorship, museum education, or management".
 
What I gathered from my reading this and other sources is that an MA/MS in a discipline is still preferred in most situations over a Masters in Museum Studies.  Many people who already have masters or PhD.'s are going back for the specialized training in a Museum Studies Certificate Program.  Lots of us are seeking the certificate in conjunction with a MA in a discipline.  My certificate program is a joint offering by the departments of History, Art History and Anthropology.  It is geared towards the study of Museology with courses in curatorship, principles and practices, visitor services, education, management, etc.  My MA  will be in in History. It is a 2 year program (if you go full time).  Most people are working in my program and so it takes about 3 years to complete.
 
According to the above mentioned book, Museum Studies programs have been around since the 1920's, but I had not heard of them either until I started my research (so don't feel alone).  Plus, I don't think they were generally accepted as valid courses of study until just recently.  Ironically, I used to work at a non-profit gallery in which the director had a Masters in Museum Studies from UC-Berkley and she was in her 40's or 50's then (10 years ago), but I didn't even remember this until I was accepted.
 
By the way, my program is at the University of Missouri - St. Louis (http://www.UMSL)  Hope this info helps. 
 
Best of Luck,
 
 
Lori Allen,
Graduate Student, UMSL