Apparently the history now allows for duplicates to exist, and when a string matches these duplicates, both (or more I guess) will be displayed as results. As you can see in the picture, I do have the 'Remove duplicate links to same target application' ticked. In my case the duplicate item is a folder, though, and the issue does not seem to exist with links to applications.
Also, I have noticed in file browsing mode, the folder being currently browsed is always converted to lower case, is that intentional? I have attached a screenshot that illustrates this behavior. The folder is actually name FaRr, but once browsed it is displayed on top as 'farr'. If this was done to make it obvious this is the folder being browsed, please make it italic or bold instead of changing it's case.