in parts reproduced with Inkscape 0.47 r22583 and Inkscape 0.47+devel r9020 on OS X 10.5.8:
The bounding box initially is displayed correctly, only after dragging the objects it gets offset from the moved object. Inkscape's status line incorrectly tells each selected box to be a group - the 'Ungroup' command however fails without further explanation.
Closing as Fix released. In Inkscape 0.92.4 and 1.1-dev (6b4d57f, 2020-04-01), trying to move on of the letters is denied with the message "Embedded SVGs cannot be transformed". The bounding box is correct, even after manipulating an object inside the nested SVG.
Thanks for attaching the file to show the problem.
Confirmed with Inkscape 0.46+devel build Jan 27, 2008.