First of all, rebuild disk? From which program?
Secondly, check your autoexec.bat and your config.sys for any new entry, may be it is called from there.
If the window starts from within Windows, check your directory on drive C: for a tree which may be called WINDOWS UPDATE SETUP FILES or similar, Bill Gates likes these confusions.
If it is from within Windows, there may be an entry in the Registry which calls this file. In this case we have to search there.
Please keep us informed, we may be able to help.