I have a problem that been reported before but the solution on that page has not helped me at all. Basically, Synapse can't find ANY* files or folders other than "Home" and I've never been able to figure out why. This means I am limited to using it to open apps. When I want to find a file or folder, I still have to navigate to get to what I'm looking for. And I've finally had enough!
I use Ubuntu 12.04 LTS on three machines (a laptop, a desktop, and a VM) with Cinnamon (edit: Unity too), and Synapse doesn't find files or folders other than "Home" on ANY of them. This has been driving me crazy for so long, and I keep coming across this answer every time I try to solve it, but it just doesn't work.
Footnote: Correction - Synapse can find some files (but very few), and no folders other than home.
UPDATE: Seriously, people. Nothing? Nada? Not even a wild guess? If it doesn't work on multiple machines for me I can't imagine no one else has had this issue! I was thinking maybe Spideroak or Dropbox was interfering, but I disabled them and ran the zeitgeist commands in the linked page, and still nothing! Gaaa! I feel like I'm living in the stone age without this!