Typically the reason is often the need for radiation hardening. Operating in space, or on the surface of Mars, outside the radiation shield that is the earth's magnetic field, is a very different, and very harsh, environment for electronics.
> Due to the extensive development and testing required to produce a radiation-tolerant design of a microelectronic chip, radiation-hardened chips tend to lag behind the cutting-edge of developments.
http://en.wikipedia.org/wiki/Radiation_hardening
Pertinent quote from the above Wikipedia article:
> Due to the extensive development and testing required to produce a radiation-tolerant design of a microelectronic chip, radiation-hardened chips tend to lag behind the cutting-edge of developments.