AS works until the file is saved

I am a high school web design teacher and we are working with Flash CS4 for the first time (we are migrating from Macromedia 8)

Here is my problem, some students have actionscript that works until after they save. There are no compiling errors, the buttons work fine.

At the end of class, the students save their work and then reopen the file the next day and the buttons no longer work. This only has happened to a handful of students.

I was beside a student, he finished his project, saved it without closing, and the project would no longer work.

Any thoughts? Is there something I should be telling them regarding preferences?

Thanks for your help.