If you have constructed your model correctly, I expect the results of the two simulations to be equivalent but not numerically identical. Here's what I mean. When you change the stop time form 250 day to 6000 hour, you will change the time units used for logging the simulation results. So, the results in the first simulation at a time of 1 (day) will correspond to the results in the second simulation at a time of 24 (hour).
If you still see a difference you don't understand, then you will likely need to share more details. If you can share your project and code, that would probably be the easiest way to help. If you are unable to share this information publicly on MATLAB Answers, could you share it with me privately or with MathWorks Technical Support?
-Arthur
