the easiest explanation for this would be if you are using library blocks and somehow one of you have different libraries, however, I don't think that is your issue in this case. Given your debugging, it sounds like there is a variable that should be changing. When you say variable, do you mean Simulink signal value, or are you writing to the matlab workspace from your simulink model? Is this variable a mask parameter for those subsystems or something in the model workspace? Also, are you using model references? It is possible that something isn't getting updated. You can delete the slprj folder and try rebuilding the model as something easy to check. You could also try deleting all the .slxc files just in case. Can your provide examples of the particalar variable that isn't changing?