$ uname -a
Linux NXOR 3.17.1-1-ARCH #1 SMP PREEMPT Wed Oct 15 15:04:35 CEST 2014 x86_64 GNU/Linux
$ inkscape --version
Inkscape 0.91pre2 r13629 (Oct 20 2014)
If path Y has the "Clone Original Path" effect applied with the cloned path being path X, and I select both paths and transform them, path Y will have the transformation applied twice. It will move twice as far, rotate twice as much, etc. If paths X and Y are grouped, and that group is transformed and then ungrouped, path Y will have the group's transformation applied twice, as well.
The attached file simply has a transformed group of a fill and a stroke that clones the fill. If it is ungrouped, the stroke will "jump" away.
If I had to fix the problem, I would make it so that whenever a path has a transformation applied to its nodes, all paths that clone it will have the opposite transformation applied.
On OS X 10.7.5:
- reproduced when using the sample file in Inkscape 0.91pre3 r13670
- reproduced when recreating the example from scratch in a new file in 0.91pre3 r13670
- reproduced when using the sample file in current trunk (0.91+devel r13845)
- not reproduced when recreating the example from scratch in a new file in current trunk r13845
(trunk uses 'Fill between many' instead of 'Clone original path' for the same cloning effect)