Hi there, hi @haydenyoung,
we currently see a similar problem. We run a multi-journal OJS installation (3.1.0.1) and the search is working with all our journals that publish articles submitted by using the standard workflow. However, search is not working with one of our journals, where we publish articles by native xml import of whole issues. Could there be a relation to the problems described in the former posts?
Cheers,
Sleipnir
Edit: @bozana
I put you here because in the question Problem with search after upgrading to OJS 3.1.0.1 you asked for different workflows publishing articles. Maybe you could also help here 