I can confirm this as well it is incredibly frustrating and slowing me down.
Evernote Version 6.12.1 (455453 Direct)
PLEASE Resolve this!!!!!
If you are working in another app and fats switch back to Evernote it returns you to the main Evernote window. NOT the last Evernote window you had open. IE I open a note to work on it in its own window, go to another app ie chrome then switch back it does not return to the original Evernote "Note" window but the main Evernote window, meaning that I have to then mouse back to the window I actually need.