In addition to what Natalie has suggested, you should also remember that the goal of user research (and usability testing a prototype is a form of research) is to understand your users better. So what assumptions are you making about your users that you need to validate?
Also keep in mind that creating a series of isolated prototypes might be useful for testing individual use cases, but if you were able to put together a more comprehensive prototype that accounted for a range of use cases in one, it’s going to be a more [I]believable[/I] prototype, and will allow the user to explore, discover and “play” (and hopefully do something you weren’t expecting). People are non-linear, so if you just create a prototype that lets them do one thing and blocks everything else, then you’re not going to learn as much because you’re already funnelling them down a certain path. Of course you have to give them a task to complete, but you may be missing some of the biggest opportunities to gain insights about how your users think.
Hope that helps.