The initialization runs twice if "Icons & Ports"-->"Run initialization" is set to "On" or "Analyze" (assuming MATLAB detects the initialization needs to run). When the initialization runs twice, the order of execution seems to be:
- Run "Initialization"
- Run "Icons & Ports"
- Run "Initialization"
![](https://www.mathworks.com/matlabcentral/answers/uploaded_files/180284/image.jpeg)