How are you running those keyword searches? If you're running from the Keyword Search Bar at the top right of the UI and you haven't ran the Keyword Search module, then the Solr index hasn't yet been created and your searches won't work as expected.
It sounds like you've already ran the Embedded File Extraction Module. If not, run that first. After that, you can either build your keywords as a list in configuration settings (Tools > Options > Keyword Search) and then run the ingest module, or run the ingest module (even with no lists selected) to generate the Solr index. As long as embedded files have been expanded and the Solr index exists, either the Keyword Search module or the Keyword Search Bar should work for you. You can configure Keyword search, then run all pertinent modules at the same time, of course. I'm explaining them linearly so it makes sense (hopefully).