What in the world did they do for $12,500?!! Do you have any idea of what may have been done to the house just prior to the roof leaking? Do you have an attic that you can get into? Did the Contractor resort to 'cutting into' the drywall, and such, to try and trace the leak? Does it leak ONLY when it rains?
From here, it's hard to tell what's going on. At this point, I think it's necessary to start cutting into the wall(s) to trace the leak assuming all other 'visual inspections' are complete. Now, if you KNOW where the leak is coming from but can't fix it, then tell us what you know. It MAY be possible you have a 2nd leak, no???