I use a handful of files fairly often but Gnome-do can never seem to find them. Documents/foo/Infrastructure/cheat-sheet.txt never comes up when I type "cheat-sheet" though it is right there if I do locate cheat-sheet and I have no trouble bringing up the directory it is in ("Infra..." and it is right there).
What might be going on? Needless to say, this is kind of annoying.
I'd suggest checking the config for your "Files and Folders" plugin. The "Depth" setting on your Documents folder may not be high enough to get down to that level.
Start gnome-do from command line and see if you get any error messages.
There are comments on launchpad where gnome-do did not work due to a plugin going into an error. 2 examples I found: "Could not locate Skype on D-Bus. Make sure Skype is running" and a uTorrent shortcut in '.local/share/applications/wine' that had invalid encoding. Both users found these errors when gnome-do was started from command line and starting skype and removing the invalid torrent file made gnome-do work again.