As Goafan said, the AI doesn't play well on maps with large distances between colonizable gravity wells; multistar maps are the most common case, but the AI will display the same problems on a single-star map if you, for example, place a very good planet incredibly far away from all other gravity wells. It is important to note that the AI cares about distance only: for example, even if you have a wormhole next to said incredibly far away planet so that players could travel to instantaneously with wormhole tech, the AI will ignore the wormhole, as it sees the large distance between the two wormholes, not the instantaneous travel time between them; quite an odd oversight by the developers, if you ask me. If you still want multi-star maps, you can make sure the systems are as close to each other as possible (overlap causes displacement in the z direction, which actually makes trips longer, since gravity wells are cylinders, not spheres).
One possible work-around is to make gravity wells essentially touch each other, but reduce interstellar travel time via modding. The AI will see the gravity wells that are extremely close to each other and will be less picky about what planets it visits, but the actual travel time between gravity wells remains the same as it was in vanilla.