Notes contained in an EPSF image print in the stacking order in which they were created, not in their actual stacking order.
These Note objects appear on screen in their correct stacking order, though, so the situation isn't detectable until the EPSF object is printed.
Move the notes to the front of the stacking order, then resave as EPSF. (Click the Note tool, choose Select All, choose Move to Front, then Save As to an EPSF file.)