The following is an example of how this issue can appear:
When using the BeagleBone Black support package with a model containing a Pulse Generator block, let us say initially that the sample time of the Pulse Generator block is set to 0.1 seconds. In this model, the LED turns on and off with a period of 1 seconds. Then, we compile and run the model on the BeagleBone Black. The LED period seems fine. Now, let us change the sample time of the Pulse Generator to 1 second. In this case, the LED blink period should be 10 seconds. However, when the generated executable is deployed to the BeagleBone Black, the LED blink period does not change.
1) Delete the code generation directory and try building the model again.
2) Install the latest version of the support packages.