This may be an issue with either your toolbox cache not being up to date or having insufficient privileges to your pathdef.m file.
Try running the following commands in MATLAB:
>> rehash toolboxcache
>> savepath
Afterwards, try starting up MATLAB Compiler again. If the above commands return with any error about permissions error with the pathdef.m file, try placing the file in your MATLAB working directory.
The pathdef.m file should be located in your $MATLABROOT\toolbox\local (for Windows) or $MATLABROOT/toolbox/local (for macOS and Linux).
$MATLABROOT being your MATLAB installation directory.
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