GalCiv hasn't broken save file compatability since beta4, but the changes have occasionally been significant enough that a game from an eariler version gets really strange. As one example, a game from 1.02 going into 1.03 had severe morale problems because of changes in the morale calculations, and it was usually very difficult, at best, to repair in game.
Smiliarly, a game going from 1.03 to 1.04 would have had morale and income problems from the removal of the PQ bonus from six of the techs if the game was far enough in that any of the players had post-Terraforming techs.
I don't know if any of the changes in 1.09[b] would cause something like that or not.
~SDC~