I had this problem, then found a solution, this note is just to vent a little, and perhaps save others a little irritation. This topic may be a little geeky probably not too useful for beginners.
The indexer or search or something (I suspect indexer) does not work in Junctions, until you push it a little--if you create a junction to a location, say to folder-X, that junction will for many purposes work as a substitute for folder-X. A glaring exception, is that the search on that junction will return zilch, nada, zip.
Why was I using junctions in the first place? I was testing life as a Standard User (in Vista etc was called a Limited User). It was easy to start up a Std Usr account, but I wanted access to my old documents, and, I did not want to have 2 copies of thousands of documents in my "real" account and in my "Standard User" account. Would be a version control nightmare.
I had found the Junction utility earlier Junction v1.05
and found it promising, but was not sure where to use it. Now I had a use. I went to my original "Real" account, and gave my Standard User account access to my documents. Then
C:\Users\StandardUser> Junction Documents c:\users\RealUser\Documents
Now all my documents were accessible whichever account I was logged into. But search did not work in my Std Usr account. I fought this quite a while. At first I thought that it was a privilege issue, I deleted and rebuilt the index twice, still no search (at least, where I was always searching--somewhere in my data) Except that I did have one search result, after I edited one of the documents from the Std Usr account. The light came on, I realized it might be the junction problem, and I tested a few documents of negligeable importance, dragging them from c:\users\RealUser\Documents to C:\Users\StandardUser\Documents.
Note that the documents dont really move, the Junction (symbolic link, what ever you call it) is like a wormhole, for most purposes, the documents are already in both places, even thought there is only one copy of each document. Whatever, it worked, so I dragged a folder, it worked, then I dragged all my documents--Viola! All documents accessible from each account, and Search, as near as I can tell, is working fine. And working as a non-admin user is looking better all the time.
This forum is teriffic, and I have solved many problems just by lurking here. But now and then it is nice to solve one for myself.