PointSetVtkMapper2D deletes all translation elements of the point set geometry. Furthermore it seems like the geometry used for rendering isn't kept up-to-date.
The current workaround is to use the old point set mapper:
m_DataNode->SetMapper(mitk::BaseRenderer::Standard2D, mitk::PointSetGLMapper2D::New());
This bug is very release relevant because point sets are a fundamental datatyp used in many plugins.
[25f573]: Merge branch 'bug-15921-PointSetVtkMapper2D-Point-transform'
2013-09-18 16:36:12 Sandy Engelhardt [266de2]
Add a new Test for PointsetMapper2D with transformed Points
2013-09-11 15:40:13 Sandy Engelhardt [4a67a7]
transform pointset according to the datanode geometry
Stefan, it would be nice if you could test the transformation in your module at some point and let me know whether there are further issues. Thanks!!