I agree with Dmytro.
If you change manually the hierarchy of mapped object by drag and dropping them to their grand parents, that will not work.
According to support page, you have to enable Extended find on a child, and delete his parent. When confirmation dialog popup, simply click no to keep children object mapped.
The thing is, even if you follow instruction of the support page
http://support.smartbear.com/viewarticle/12466/, you may have others difficulties using them as I wrote earlier
http://community.smartbear.com/forum/post/?mode=singleThread&thread=75c33127-e966-4d05-8088-8178db103112Regards.
