According to the screenshots (blank System.ini) I am guessing the infector either replaced it and/or had the registry pointers point to the variant instead.
So even if the CWShredder removes the bad one but afterwards normal startup is re-enabled, the infected System.ini will re-infect and replace the msconfig executable yet again, it is a loop.

You will have to do the steps in the link that Judy gave you and then attach all the log files....