Some information for you to consider -

Is it DOS related or Auto Play related for Trojan related?

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.
Error message when you install or start an MS-DOS or 16-bit Windows-based
program
http://support.microsoft.com/?kbid=324767

Replace the standard version of autoexec.nt/config.nt by copying a backup
copy located in %windir%\repair\ to %windir%\system32\
(NB: %windir% is typically C:\Windows)

Start>Run and type in this without the quotes:
"cmd /c copy /y %windir%\repair\autoexec.nt %windir%\system32"

Troubleshooting MS-DOS-Based Programs in Windows
http://support.microsoft.com/default.aspx?scid=kb;EN-US;314106

16-bit MS-DOS Subsystem error while installing or running a DOS application:
http://windowsxp.mvps.org/16bit.htm

Can also be caused by a Trojan - please scan your computer for viruses etc.

Autoplay Repair Wizard
http://www.microsoft.com/downloads/details.aspx?FamilyID=C680A7B6-E8FA-45C4-A171
-1B389CFACDAD&displaylang=en
or
http://tinyurl.com/4f2mx
The Microsoft AutoPlay Repair Wizard scans your computer devices to find
defective AutoPlay settings, and attempts to fix those it finds.
Supported Operating Systems: Windows Server 2003, Windows XP

Why doesn't AutoPlay work?
http://www.kellys-korner-xp.com/top10faqs.htm