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MATLAB creates a local process pool with some default name. If you fire up a second copy of MATLAB on the same machine, it will use that same default pool so the two different copies will compete/conflict.
Here is a bit of MATLAB code that will create a pool whose info is stored in a specified directory and hence won't conflict:
mkdir('/tmp/fowlkes.1');
schd = findResource('scheduler', 'configuration', defaultParallelConfig);
schd.DataLocation = '/tmp/fowlkes.1
'
matlabpool(schd);