path and user preferences not saved between Matlab sessions

I run Matlab on Mac by directly calling the binary in this location:

/Applications/MATLAB_R2017b.app/bin/matlab

Unfortunately Matlab is not saving my path settings in between sessions even when I type "savepath". It also does not seem to save my user settings in the Preferences window. It seems like I have two pathdef files and Matlab might be editing the wrong one? How do I fix this? Another explanation is that Matlab is resetting my path file every time I close the program and call a new instance of Matlab.

>> which pathdef -all

/Users/stockmann/Documents/MATLAB/pathdef.m

/Applications/MATLAB_R2017b.app/toolbox/local/pathdef.m % Shadowed

[Jan]

Do you have write access to these files? What happens when you start savepath? Do you get an error message? Do you have write access to the preferences folder prefdir? Are you working on a virtual machine, which resets all changes at a restart?

[Jason]

Thank you for your reply. I'm running Matlab locally on my Mac. And yes, I have write access to the preferences folder prefdir. When I run savepath, it returns a 0 "file saved successfully".

[Jan]

@Jason: If savepath runs successfully, it has written the changes to /Users/stockmann/Documents/MATLAB/pathdef.m - please check this manually. Now the changes here are not applied, when you restart Matlab - correct? Then Matlab prefers "/Applications/MATLAB_R2017b.app/toolbox/local/pathdef.m" at startup instead of the user defined version. Then the actual problem is the startup folder of Matlab.