using Scrivener 2.5 on Mac OS 10.9 And it is the Project Replace. When it didn't work (several times, naturally, trying words that were before me in the document) I used Find, and that worked w/no problem. I didn't have this problem in the last version of Scrivener.
My replace function isn't working either, though find seems a-okay. For what it's worth, it used to work. All boxes checked, says "not found." (I tried various iterations of caps and no caps, still no replace.)