The question is how Matlab is affecting your app's behavior, since it's a separate process. I suspect Matlab is modifying environment variables in a manner that affects OMP, maybe because it uses OMP internally, and the process you are spawning from Matlab is inheriting this modified environment.
Do a "set > plain.txt" from the command window where you're launching you app plain, and "system('set > from_matlab.txt')" from within Matlab, and diff the outputs. This will show you the differences in environment variables that Matlab is introducing. When I do this, this appears in the environment inherited from Matlab, but not in the plain command window's environment.
OMP_NUM_THREADS=1
That looks like an OpenMP setting related to the function calls in your question. I'll bet your spawned app is seeing that and respecting it.
I don't know why Matlab is setting it. But as a workaround, when you launch the app from Matlab, instead of calling it directly, call a wrapper .bat file that clears the OMP_NUM_THREADS environment variable, or sets it to a higher number.
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