Comment 3 for bug 582716

@Miro - here's a solution if you are using a recent development build: Clipping and Masking has a new option to place the clipped or masked objects automatically into a new group (which is automatically ungrouped when releasing the clip or mask, and allows easier editing of - as well as adding new objects to - the clipped or masked content). Wrapping the transformed object in a group before clipping has the side-effect that the clip-path itself is no longer transformed as well because now the clipped object (the group) doesn't have a preserved transformation matrix. The resulting clipped object looks as expected, independent of the 'Affect:' setting to scale the radii of rounded corners.

Setting to change:
'Inkscape Preferences > Clippaths and Masks > Before applying clippath or mask:'
[x] Put all clipped/masked objects into one group