Transfer of mitochondrial and chloroplast DNA to the nucleus

As a logical conclusion of the endosymbiotic theory, since modern-day mitochondrial and chloroplast genomes do not contain a full set of housekeeping genes, and lack many that other descendants of their speculative ancestors share, there must have been a loss of genes. However, some of these genes likely migrated to the nucleus, where analogues of these genes are now found.

Puzzle
It is not clear why only a subset of genes have been transferred, when such gene transfer is known to be rapid - on a similar timescale as mutation. Mitochondria and chloroplasts perform redox reactions, which are known to be considerably mutagenic. Such mutagenicity would encourage migration of genes away from the organelles to the nucleus.

Proposed explanations

 * Since chloroplast and mitochondrial genetic codes differ slightly from the eukaryotic nuclear code, some genes may lose function when they are transferred.