16 bit Windows Subsystem
C:\WINDOWS\SYSTEM32\AUTOEXEC.NT
error message in Windows XP

If you get an error message similar to:

16 bit Windows Subsystem
C:\WINDOWS\SYSTEM32\AUTOEXEC.NT.  
The system file is not suitable for running MS-DOS and Microsoft Windows applications.  
Choose 'Close' to terminate the application.

(note: see the message at the bottom of this page for a quick way to fix the problem) 

I found the following two articles at microsoft.com:

http://support.microsoft.com/kb/324767

http://support.microsoft.com/kb/305521

The articles basically say you need 3 files in the system32 folder in your WINDOWS folder:  

Config.nt
Autoexec.nt
Command.com  

The first step would be to see if all three files are on your computer in the WINDWS/system32 folder (on your C drive).  Even if they are, it sounds like one of them could become messed up for some reason.  

Of all the solutions they have, re-installing the 3 files from your Windows CD seems to be the easiest - although I don't know why any of those files should become messed up or be missing.  

To re-install the files: (note: see the message at the bottom of this page for an easier way) 

1. Insert the Windows CD into the CD drive.

2. Click Start, and then click Run.

3. In the Open box, type cmd, and then click OK.

4. At the command prompt, type the following commands, pressing ENTER after each command:  

expand CD-ROM Drive Letter:\i386\config.nt_ c:\windows\system32\config.nt
expand CD-ROM Drive Letter:\i386\autoexec.nt_ c:\windows\system32\autoexec.nt
expand CD-ROM Drive Letter:\i386\command.co_ c:\windows\system32\command.com
exit    

CD-ROM Drive Letter would on most computers be the letter D, so you would type:
expand D:\i386\config.nt_ c:\windows\system32\config.nt
You can check to see what letter your computer uses for the CD drive by clicking on the "My computer" icon on your desk top.

An Easier Way to Fix the Problem

If you don't want to re-install the files from your Windows CD, or just want an easier way, I found a web site that has the installers for the missing files (Win 2000, XP Home, XP Pro). Just click here to go to the WebUser web site and download the installer you need.