I know I've seen this problem mentioned before. Have you every been attempting to plot to .pdf when Revit decides that regardless of what settings you have, it will plot each sheet/view as an individual file?
In order to avoid this mess, make sure that the last place that you click the mouse is inside the window of any printable View. That's it! This problem arises when the last place that was clicked in was the Project Browser, which confuses Revit (which isn't exactly a feat). This is likely a combined result of Revit trying to plot the selection(s) from the Project Browser and having a list of sheets queued under the Print dialog.
If anyone can confirm or debunk this, please post!