I have a bookmark called PB and a bookmark called PT. These are work bookmarks, and I use them often. Before, I used Alfred and it worked very well. No matter where I was, I'd hit CMD+Space and type PT and I'd get my bookmark launched. With Yosemite, it worked until I hit return too soon and it opened a file beginning PT. Now, even though Safari bookmarks are above files in my Spotlight list settings, that file still pops up first, and now, Spotlight shows bookmarks containing PT but not the actual bookmark named PT. So I think Spotlight has noted that I opened a file called PT rather than the bookmark PT, so it moved that up the list, overriding my requirement that bookmarks appear top. Why it no longer shows the PT bookmark at all in Spotlight baffles me though. Might need to switch back to Alfred for now. It didn't learn much about how I used it, but at least it did showed me matches properly, rather than trying to be too smart.