Are you use the Fast Forward content type (rffFile) or have you created your own? I would check to see if you logged into the right community to which the content you are searching for belongs. Also, you may not have visibility because of the workflow state the content is in.
It sounds like you’re saying that you do get some search results from rffFile content items, but the result set doesn’t contain all the results that you expect it to.
One possibility, the content items that are not showing up in search results have never made it to the Public (publishable) state in your workflow. I believe that items aren’t added to the Lucene search index at all, until the first time they encounter a publishable state in the workflow.