Solema, just to be sure. Are you renaming the config file when you enter your stats/rotation or are you using the gui?
If you are renaming the config, make sure the sim is running with the correct config file. Your output looks exactly like what the default config gives, so your probably not using the correct file name.
If you edit 'start_simulation' and is shows this:
enhsim.exe config.txt output=output.txt
then make sure to change 'config.txt' to the name of your altered config file.
For example, when I run the sim I create my config file called 'config-enh.txt'. Since this is the name of the config I want the sim to use, I have the following in the 'start_simulation' batch file:
enhsim.exe config-enh.txt output=output.txt