I've been experiencing the same problem with DNN 4.8 and Repository 03.01.13. I looked at Gemini's issue REP-1963 and discovered that it was "withdrawn" with reason "cannot reproduce". Why?
All my repositories have multiple categories. When searching, titles of documents come up, but when I click on the link it takes me to the page that hosts the repository module where I see a repository having the "ALL" category enabled, but without any documents! (There actually are documents belonging to the "All" category). If I select a different category from the dropdown, then documents appear. Of course, if I re-select the "All" category, documents appear normally.
This is a major bug IMHO, due to the fact that search results mislead the user to believe he's navigating to an empty repository.
I'm using the filelist skin.