I am aware that frequently clones have genetic defects not present in the donor organism, even though the two are genetically identical. The reason for this is that apparently the enclosing gametocyte "reprograms" the genes inside of itself and during the cloning process, this reprogramming is not completed because the novel DNA is in the host gametocyte for too brief a period. Here is a quote from an article on the subject:
In cloning, scientists slip a cell from an adult into an egg with its genetic material removed. The egg then reprograms the adult cell's genes so that they are ready to direct the development of an embryo, then a fetus, then a newborn that is genetically identical to the adult whose cell was used to start the process.
What do they mean by "reprogram" the cell's genes? How can a germ cell modify its own nucleus in a way that would not affect the base pair sequencing?