If you have not already done so, try using the Simulink debugger.
Instead of clicking the Run icon on the toolstrip, click the Step Forward icon.
Then right-click on the key input and output signals and select
"Show Value Label of Selected Port"
to get little yellow boxes showing the current value of the signal.
For this portion of your model:
>> I set up my own counter, not using any counter blocks (I did it using a Constant, Add and Memory blocks).
stepping through the simulation is likely to be especially helpful because you can see all the details.
If you need to control input values, then consider using Repeated Sequence Stair Blocks. I find these very helpful in debugging, because they allow me to isolate things and quickly get to interesting sequences of inputs.
Hopefully, single stepping using the Simulink debugger will allow you to quickly find a point where the model's actual behavior does not agree with your mental model of how it should behave. Once you've isolated where the disagreement begins you'll likely be able to resolve things.
If you can't resolve it own your own, try to create reproductions steps that are as simple as possible. For example, remove everything from you model not necessary to reproducing the disagreement. Also seek to highly simplify any external dependencies like M files and MAT files that define parameters used by the reproduction model. The fewer external files and parameters the better. Then share the simplified reproduction model with others. For example, up load the highly simplified model and all necessary supporting M file, MAT files, non-MathWorks Simulink libraries to MATLAB Answers. Nothing slows down getting a helpful answer more than not providing all the needed items another person would require for reproduction.
When I upload reproduction steps, I find it very helpful to "dog-food" the steps. I download the reproduction items to a clean directory, check my MATLAB path just includes things from the MathWorks install and not specific to me or my group. Then I go through my own reproduction steps. Around 40% of the time my dog fooding shows that I forgot to upload something in my first and sometimes 2nd and 3rd attempts to provide usable reproduction steps. The dog fooding usually saves many days of frustration for me and the people seeking to utilizing my reproduction steps.
Hope the debugger solves your issue.
