A 1998 Los Alamos release
"...the anomalous motions of these spacecraft are so small that the researchers had to consider numerous possible causes: perturbations from the gravitational attraction of planets and smaller bodies in the solar system; radiation pressure, the tiny transfer of momentum when photons impact the spacecraft; general relativity; interactions between the solar wind and the spacecraft; possible corruption to the radio Doppler data; wobbles and other changes in Earth's rotation; outgassing or thermal radiation from the spacecraft; and several others.
The researchers have so far not found that any of these effects can account for the size and direction of the anomalous acceleration.
After exhausting the list of possible "normal" explanations, the researchers looked at possible modifications to the attractive force of gravity or the possible influence or non-ordinary matter, or "dark" matter.
The dark matter explanation didn't hold up because so much matter would have been required to create the measured spacecraft acceleration it would have affected motions of other bodies in the solar system.
Looking at other mathematical representations for gravitational interactions also "come up against a hard experimental wall," the researchers wrote: namely that the gravitational effect would also be seen in planetary motions, especially for Earth and Mars... "