If you don't want to do this surgically, you can restore the most recent CAB file, which contains your registry and system.ini. To do that, type scanreg /restore at the MS-DOS command prompt.
Also, applications that write to system.ini will often make a backup copy of the file before changing it. Start the computer to MS-DOS, then look in C:WindowsSystem for system.bak, system.tmp, etc. If the file looks like your system.ini, restore it. Also, if you find multiple backup copies of system.ini, restore the latest version.
No matter how you restore system.ini, you're going to lose any changes that were made to the file since the backup.
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This was first published in March 2002