There is a difference between the two. I know this because I have been on both. The waitlist is applied once you have interviewed and they do not want to make a decision on your case. Most schools will place you on the waitlist after an interview if they think that they may be interested in you after they have interviewed a certain percentage of the applicants. In other words, you are neither rejected or accepted. I was placed on the waitlist to Marshall University in October and still have yet to hear from them.
The alternate list is a list of ranked, or in some cases unranked individuals, that did not get a spot in the class outright. The create alternate lists in case one of the people they accepted decides to pull their acceptance late in the game. This is how they insure that their class will be filled at the time of matriculation. I was placed on the alternate list two years ago at WVSOM and found out the day before their classes started that I had not been moved from the list and therefore did not get accepted.
Both are good things to be on, because they signify no rejected applications. I have known several people who got accepted in August for the upcoming school year because they were on the alternate list. Dont give up, even though you constantly check your mail and phone machine to see if you have heard. Most of the time, no news is good news. I hope this helps. Feel free to PM me with any additional questions.
Aaron