Hey Seereen,
Here are some possible workarounds to the problem you're facing -
- https://www.mathworks.com/matlabcentral/answers/125476-why-can-t-i-use-the-command-publish-or-open-up-simulink-in-matlab-r2014a
- https://www.mathworks.com/matlabcentral/answers/112741-matlab-errors-when-attempting-to-publish
These are instances with a similar issue that you describe. The workarounds are mentioned in these links.
Hope this helps!