[wrapping up off-line discussion]There does seem to be something odd with the pdf. (Copying the note to other pdf files and saving as pdf or pdfd files and then embedding does not show this problem.)
The remedy is to, after exporting with notes embedded: Open that embedded file and convert notes (i.e., File:Convert Notes).Restore the original text color and line width. (I attached a script to help with those restoration steps. The script is a modification of Christiaan's "Set Color of Notes" script at http://sourceforge.net/apps/mediawiki/skim-app/index.php?title=AppleScript.)
Re-embed. humanengr
%Set Text box attributes.scpt
Description: application/applefile
Set Text box attributes.scpt
Description: Binary data
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