You can start as many Matlab programs as your license allows. Running the same M-functions will not cause any troubles as long as you do not try to write to the same files. E.g. changing the preferences of Matlab or any user-define preferences files inside the prefdir folder will cause conflicts for obvious reasons. So if you keep care for such problems, running Matlab multiple times on a multi-core machine is an efficient method.
When accessing the hard disk or the network is the bottleneck, a parallel processing will not be much faster then a sequential processing.
