Not at this time. The plugin was built to tie into a specific post type, so it pulls all the posts from that post type.
Now, I suppose if you didn't mind doing some hacking, you could create a copy of the plugin, give it a different name, and modify the post type so it, too, had a unique name. Then you'd have two unique post types that were displayed using smoothdivscroll and could be used independent of each other. You'd also need to change the shortcode otherwise WordPress wouldn't know which scroll to use.
The only other way I see this working is to create your own custom template and add some kind of meta key to differentiate which scroll to display.
These are good questions, though, and this gives me an idea of how I could handle multiple different scrolls on the same site using taxonomies...I'm not sure I have time to work on it this month, but I'm definitely thinking about it and will try to add it in an update.