I recently upgraded via the Evernote site (not the app store), and I am experiencing the same trouble.
My workflow is similar: I start in Evernote, and then open a PDF using the Preview app. I highlight text, and the changes are automatically saved back to Evernote.
I highlight in Preview because it is 10x faster -- just drag to select text and it's highlighted. By contrast, with Evernote's highlight feature I have to physically draw each line using my computer, which is tedious and time consuming. Their highlight also reduces contrast and readability by covering the text in a transparent colored haze. In Preview, when the PDF does not allow highlighting I can quickly draw lines underneath that are auto-straightened.
That being said, I would much rather mark up PDF's natively inside Evernote, once they develop a usable feature.
This highlighting workflow constitutes about 70% of my Evernote usage, I hope we can figure out a way to link these again. I appreciate this company and all their hard work, I hope they can ship a usable PDF annotation feature soon!