Have MATLAB Publishing issues

I have a long script, about 10 questions, when I publish the script to PDF format, for each question up to Q8, the relevant tables and figures show up in the pdf. However for Q9 and 10, the pdf just shows the code, it's like MATLAB completely forgot to run these pieces of code.

Even when I convert the script to a live script, and run the entire live script, it does so up to Q8. To get Q9 and 10's figues to show I would have to run those sections of the livescript themselves and then they show up.

I have tested the code for both these questions in a brand new script and they work perfectly fine, so for some reason, once it's together with the entire script, it fails to run.

I am unsure if this is relevant, there are 3 function files in the directory, for which all these questions use in their code.

Is there a reason why MATLAB won't run this code during publishing, and also via live scripts?

Any help would be appreciated!