Sorry for late answer, You may check the below things,
- be sure that rc.txt file is located in the SD card in etc folder. In addition there must be a folder named as log.
- please check inside the rc.txt, there must be a line like "px4_simulink_app".
- May be you may run the model, there is a safety button which flahes, it must be solid in order to generate signal from PWM ports.
- for logging data, you may connect a step input to enable port of binary logger block. Aware that type of the enable is boolean, and the output of step input is decimal. you must convert it.
please try those and inform me, I will do my best.