doc library only showing 1250 records out of 7600 in the library

I have a document library that has around 7600 documents in it. When I go into the library I can only see 1250 rows. I created views but its not returning all documents that match that filter in the view, also it appears that the search is only searching the 1250 and not the full library. Other then changing the 5000 threshold, how can I get the views to return all documents matching the filter and how can I get the search to search the entire library instead of the 1250? I indexed several columns, but that didn't make any difference