The thing to understand clearly is that the table view that appears when you are doing a search with the UISearchDisplayController conglomerate is not your table view. It is a different table view, and you do not have a UITableViewController managing it - the UISearchDisplayController does that. Thus you must take other measures if you want that different table view to look like your table view.
EDIT: On the whole (and after the little exchange with rdelmar in the comments on his answer), I tend to think the easiest solution is to abandon the use of cell prototypes altogether. If you design the cell in a nib (xib), you can then use that cell both for the real table and for the search results table. In both cases you register the nib with the respective table view - and then dequeue
just does the right thing all by itself, in both cases, with no change in the code.
You can see me doing something similar here:
https://github.com/mattneub/Programming-iOS-Book-Examples/blob/master/ch21p632searchableTable/p536p550searchableTable/RootViewController.m
... except that in that case I'm registering the same cell class for both tables, not the same nib. But it all comes down to the same thing. However, note that I do not start with a storyboard, so I never fell into the trap of using a prototype cell in the first place.