I'm calling mathematica scripts running kernels through a cygwin terminal, which are again executed from c++ code. When I do this a window pops up, prints warnings and errors if there are any, and then disappears when the computation is done.
This gets annoing because the window automatically opens on top of whatever else I'm doing. I've tried to find solutions without any luck - for example this thread gives the answer for some other situations but wouldn't work from cygwin I think.
EDIT: To clarify: I'm trying to run a Mathematica script from the cygwin terminal without a Mathematica window popping up. That is, I'm running a command in cygwin with something like
./MathKernel -script myScript.m 45 3 where 45 and 3 are parameters in the computation. Everything works fine but a Mathematica window pops up un top of everything and disappears after a little while, something I'd like to avoid.