This line appears to be the culprit:
(define-key map [(control m)] 'newline-and-indent)
With that line turned on (as is the case with r524 and earlier), bug #670674
appears. With it commented out, this bug #670701 appears as in r525+.
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https://bugs.launchpad.net/bugs/670701
Title:
Multiline copy including comments cause trailing whitespace to be
pasted
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