If you specify an executable for the command line modules plugin (preferences->command line modules->additional modules) it checks if the executable responds with proper XML when called with the '--xml' argument. If there is no response for a while, the debug console says the process has timed out.
However, in my case it is a Matlab executable which typically takes a long time to respond because of the Matlab compiler runtime. It took several seconds even when I launched the exe (with '--xml') in cmd.
Unfortunately I cannot give you the precise debug output as I'm not able to recreate this scenario because the Matlab executable in question responds a lot faster on the second run.
I feel the timeout period should be longer - at least for Matlab executables.