We present results obtained by applying our BAyesian HierArchical Modeling for the Analysis of Supernova cosmology (BAHAMAS) software package to the 740 spectroscopically confirmed supernovae of type Ia (SNe Ia) from the "Joint Light-curve Analysis" (JLA) data set. We simultaneously determine cosmological parameters and standardization parameters, including corrections for host galaxy mass, residual scatter, and object-by-object intrinsic magnitudes. Combining JLA and Planck data on the cosmic microwave background, we find significant discrepancies in cosmological parameter constraints with respect to the standard analysis: we find W = 0.399 0.027 m , s 2.8 higher than previously reported, and = - w 0.910 0.045, s 1.6 higher than the standard analysis. We determine the residual scatter to be s = 0.104 0.005 res . We confirm (at the 95% probability level) the existence of two subpopulations segregated by host galaxy mass, separated at, differing in mean intrinsic magnitude by 0.055 ± 0.022 mag, lower than previously reported. Cosmological parameter constraints, however, are unaffected by the inclusion of corrections for host galaxy mass. We find s4 evidence for a sharp drop in the value of the color correction parameter, ( ) b z , at a redshift = z 0.662 0.055 t . We rule out some possible explanations for this behavior, which remains unexplained.