I am also having this problem. In the past, the "searching PDF" appeared for a moment and then highlighted the different occurrences of the term in the note. Now, the "searching PDF" never goes away. this is very irritating and impairs productivity when searching documents.
I completely agree with wjpreston. I am also asking for a response on when I will be able to annotate JPEGs and PDFs with Apple Pencil/iPad Pro on my Evernote App.