I have been having this same issue. My solution, only because I have an iPad as well, is to only annotate on the iPad version of Evernote. On Mac (with EN 6.10) I just view the annotated PDFs. I am not able to annotate on the Mac side, messes things up, sometimes creates a second note, sometimes a second file within the original note, but never allows me to annotate on both platforms.
If this is fixed in 6.11 beta, how do you get the beta? NEVERMIND! I found it...and happy to see that it now has working Tabs!!