Previous research [S. J. Pollock et al., Phys. Rev. ST Phys. Educ. Res. 3, 1 (2007)] showed that despite the use of interactive engagement techniques, the gap in performance between males and females on a conceptual learning survey persisted from pretest to post-test at the University of Colorado at Boulder. Such findings were counter to previously published work [M. Lorenzo et al., Am. J. Phys. 74, 118 (2006)]. This study begins by identifying a variety of other gender differences. There is a small but significant difference in the course grades of males and females. Males and females have significantly different prior understandings of physics and mathematics. Females are less likely to take high school physics than males, although they are equally likely to take high school calculus. Males and females also differ in their incoming attitudes and beliefs about physics. This collection of background factors is analyzed to determine the extent to which each factor correlates with performance on a conceptual post-test and with gender. Binned by quintiles, we observe that males and females with similar pretest scores do not have significantly different post-test scores (p>0.2). The post-test data are then modeled using two regression models (multiple regression and logistic regression) to estimate the gender gap in post-test scores after controlling for these important prior factors. These prior factors account for about 70% of the observed gender gap. The results indicate that the gender gap exists in interactive physics classes at our institution but is largely associated with differences in previous physics and math knowledge and incoming attitudes and beliefs.