Don't worry about it, we're here to help. The weirdness you're seeing "Microsoft windows version..." is the output of running cmd.exe. If you did a Start->Run->cmd.exe then you'd see something like:
Microsoft Windows XP [Version 5.1.2600]
(C) Copyright 1985-2001 Microsoft Corp.
C:\Documents and Settings\marto>
What you want to do with system is run a comand called glomosim, and pass an input file. So the first part in the example I gave you was to a program called glomosim.exe, if this isn't an executable you need to substite the command with whatever you want to run, not cmd.exe, so the general form of what you want to run is:
my @args = ("c:\\path\\to\\glomosim","c:\\path\\to\\input.file");
So you need to substite the path to the golomsim program and the path to the input file in the above example. In Re^2: system sub routine with windows7 I give some code to use to produce any errors. I have no idea what glomosim is, how it's executed, but if you substitute these values for the correct paths to the executable and input file we can provide further help if required.