Many studies have found gender differences when it comes to different types of math performance (girls better at arithmetic, boys better at spatial rotation) or preference for visual vs. verbal problem solving (boys better at visual, girls better at verbal). Some of these differences appear can be seen at very young ages (for instance, 1 year old boys gaze longer at 3-D mobiles, whereas 1 year old girls gaze longer at faces), even before significant differences in environmental influences (e.g. hobbies, sports) might occur. Nevertheless, substantial evidence supports a capacity to "overcome" the gender disadvantage with specific training.
In this other study, computer play seemed to help boys' mental rotation / spatial ability, but not the girls.
Researchers will probably have to look more carefully at frequency of game play, and even level of expertise that the girls reach (how one plays the game). In this German study, 82% girls were non-players (compared to 18% of males) and the girls seemed to prefer logic and "skill"-training games (83%), compared to only 17% of boys. The boys preferred action-simulation in the reverse proportion.
Spatial rotation is not just for game play, of course. In Beth Casey's review of TIMSS performances in girls and boys, spatial abilities were better predictors of performance on mathematical reasoning tasks than self-confidence about math in general. In the physics problem solving study, below, female students were more likely to correctly answer verbal questions than diagrammatic ones.
Gender, Computer Games, and Mental Rotation
Gender Gap in Math and Science
Gender Differences and Approaches to Problem Solving
Gender Gap & Mathematics
Fixing Engineering's Gender Gap
Eide Neurolearning Blog: Spatial Cognition: The Final Frontier
Spatial Training for Women
Eide Neurolearning Blog: Video Gamers & Visual Spatial Expertise - Hands of a Surgeon?