Comment 3 for bug 1679428

interrogation of the clipboard immediately after the two copy operations indicates that the error is probably happening during the copy. Below is the highly edited version of the clipboard after copying the original and the clone.
There are two significant differences:

1. the copy of the original has a <rect> tag outside the <inkscape:clipboard> tag, while the copy of the clone has a <rect> tag inside the <inkscape:clipboard></inkscape:clipboard> tag.

2. the copy of the original has a size of 377.95 with no extra transforms.
   the copy of the clone has a size of 100 with two additional transforms, one inside the <rect> element and one inside the <use> element. Both transforms have a scale of 3.7795276, so it is likely that one transform is redundant.

............................................
original copy (snipped)

  <inkscape:clipboard
     min="139.5,621.54725"
     max="518.45276,1000.5" />
  <rect
     height="377.95276"
     width="377.95276"
     id="rect3460" />

..................................................

clone copy (snipped)

  <inkscape:clipboard
     min="145.21429,121.54724"
     max="524.16705,500.5">
    <rect
       height="100"
       width="100"
       id="rect3460"
       transform="scale(3.7795276)" />
  </inkscape:clipboard>
  <use
     height="100%"
     width="100%"
     transform="matrix(3.7795276,0,0,3.7795276,5.7142859,500.00001)"
     id="use3462"
     xlink:href="#rect3460"
     y="0"
     x="0"
     style="" />