Same here! This now happens on both Mac OSX and windows 10. It's driving me nuts.
In a recent update, probably a month or so ago, it also now seems to select the main window of evernote when it syncs. So I'll be in the middle of typing a note, it auto syncs in the middle of my typing, and stops me from typing! It seems to just select evernote as a whole application instead of staying within my note and allowing me to type.
Both issues have really slowed down my productivity with the tool as I constantly have to click to select where I was to continue typing.
