Something was wrong with the settings.ini so I checked it out and it turns out to be something with the music/sound volume...

Well mine are set too 41 and 100
change and see if that works.
my settings always fudges up, so I keep a spare folder called cortex command back-up. which I use incase any vannila stuff goes wrong. Thats something mabye to think about its more stuff is going wrong

Where is your cortex command folder located? Often putting it on the desktop can solve some of these issues.

Its in Program files. Do you mean moving the folder on the desktop and running it on there?

Cortex Command in program files = Epic amount of errors.

Well I moved it to my desktop and it ran without an of my settings in place such as my registered copy...

*in vista