There are two possible reasons because your pdf files might not be indexed.
In the indexing options for files, there is an option for
Maximum File Size for content indexing. Check if your pdf files are larger as this number.
Also in the same options window, there is the button
Specify Extensions. Check if pdf files are included.
Other than that, I have asked
features@x1.com to add a
file inclusion and
file exclusion feature.