I am using the Devkit MPC5744P and I could check that the Model Based Design Toolbox 3.0.0 for Simulink has a wrong configuration for PBRIDGE clock.
By default, any model using the MBD toolbox presents the PBRIGDE clock frequency running on 100 MHz. I attached a model that verifies the clock configuration and a Freemaster file in order to make easier the visualization.
However the MPC5744P Reference Manual states that the maximum frequency configuration for PBRIGDE clock is 50 MHz, as can be checked below.
Kind Regards, Rafael Barbosa