MATLAB runs slowly and CPU exceeds 100% when running simulations
Seeing your CPU load graph (@200%) it appears your machine can handle 4 threads. Each thread can handle 100% of CPU load. 4 (virtual) cores can handle 4 threads, and 4 threads can handle a total of 400% CPU load. So 200% just means 2 cores are working at 100%.

Why they are stuck at 100% I can not tell. It might be something in your code. It might be something in the MATLAB's code. Is there some kind of debugging tool within MATLAB? You might try the MATLAB forums as well.

If your code is behaving differently on the same hardware using the same version of MATLAB tell us, then we can try to fix it from there.