@haider I had the same issue with XCode 4.3, tried the above recipe, but it did not work for me. Here is the correct answer to prevent this from happening and get it to work right:
There's a tiny row of icons to the left of the search box under the left hand nav. The first of these is a '+' (to add a file). The icons following the add-a-file icon are actually filters that can be toggled on and off. The first of these looks like a clock, and is a filter to show only-recently-modified files, the second to show files-with-source-control status and so on. I must have accidentally picked the first icon after the '+' (show only recently-modified files) and therefore had the problem. The XCode UI preserves that pick even when you close the project so closing and re-opening does not alleviate the situation.