this file shows a situation where the note shown in the attribute panel differs from the note visiblefor a script. There were about fife occurences in a file of about 500 art objects. I picked one and removed everything else, and also replaced the artwork by a plain rectangle.

To view the error, select the square and view the attribute panel
Then run this extendscript:
var doc = app.activeDocument;
var obj = doc.selection[0]
alert(obj.note)

BTW: I could set proper values with a simple jsx that sets the note from the contents of a text field