This is the exact same problem I had. Evernote is taking care of it. Btw, do your encrypted notes has checkboxes in them? Or maybe any other special objects other than text? This is the last email I received from Evernote
Tried EN for Mac 6.1 Beta. Still can't open encrypted text created in EN for Windows. Only this time, EN didn't delete the encrypted text. The text just stays encrypted.