Update 2013: Two software updates later, the problems with the initial release of MEP 2013 appear to have been fixed. The 2013 version is significantly faster than previous versions too.
More details are here.
After hours of experimentation I conclude that the Magix Movie Edit Pro 2013 is not usable for 3D editing at this time.
MEP 2013 added numerous 3D performance improvements; unfortunately, it introduced numerous defects to the 3D editing process. See details at the link.
At this time, I cannot recommend the use of MEP 2013 for 3D editing.
I am re-starting a large project back in the prior version MEP MX Plus, as its 3D support, while slow, actually worked quite well.
The problems have been reported to Magix and hopefully they will release a fixed version of MEP 2013 soon. Magix is a nice video editing package and the 2013 features, especially in terms of 3D performance improvements, will be greatly appreciated once they work correctly.