system.ini file

Is it at bootup or when you open a specific program?
Have you run an up-to-date anti-virus check lately?
Did you install any software off the net or a shareware disc recently? Malicious programs and viruses can tag along. Or you're using a file sharing program like Kazaa, etc that love to pass along viruses.
Do a Find - All files for system.ini to see if it has been moved or deleted by a malicious program and if it's there somewhere move it back to C:\Windows.
You may have to re-install your OS to fix it, after you have made sure the computer is virus and crappy software -free.