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Why am I not able to execute my standalone application from MATLAB environment

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Hi,
I am trying to run a compiled standalone application using MCR 9.5 on my computer from the command line in MATLAB. The application runs perfectly outside of MATLAB; however, when trying to run it from the command line using 'system(executable)', I get the following error:
Undefined function or variable 'matlabrc'.
Undefined function or variable 'ctfroot'.
Error in checkRequiredMCRProducts (line 22)
Undefined function or variable 'ctfroot'. Opening log file:
The strange thing is that the code and everything worked perfectly until a forced restart of MATLAB. I have tried deleting the mcrCache9.5 folder from AppData, but this did not resolve the issue.
Any ideas how I could fix the problem and run the executable from the command window?
The code I use to start the application is the following:
code_source = 'compiled';
release_number = '1.46-2'; % only works for compiled code.
release_dir = 'pwd';
executable = [release_dir,'\APP',release_number,'.exe '];
system(executable)

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