You could go to the link below and download "XP_Fix.EXE".
"This installaton program will reinstall the missing or corrupt Windows XP system files command.com, autoexec.nt and config.nt. The absence or corruption of one or more of these files causes a "16 Bit Subsystem" error.
We recommend that you download this file and save it to your desktop or to another location where you can find it. Double click on the file to run it once it's downloaded. If problem reoccurs in the future, simply re-run this program".
http://www.visualtour.com/downloads/
Another fix some have used is to do a search for autoexec.nt You will probably find it in C:\WINDOWS\repair. Copy and paste it into C:\WINDOWS\system32.
The 2 links below explain what may be causing the problem (Malware).
http://www.vtsoftware.co.uk/users/MarkDowsett.htm
http://groups-beta.google.com/group/microsoft.public.windowsxp.general/msg/a448971496ce38b5
Tufenuf
when i try to run some of my programs, i get the following message:
16 bit Windows Subsystem
C:\WINNT\SYSTEM32\AUTOEXEC.NT. The system file is not suitable for running MS-DOS and Microsoft Windows application. Choose 'close' to terminate the application.
what does this mean, and how do i fix it? I need to use these programs and now I can't. I choose ignore and that does not work. Any suggestions?
and other programs still work, but some of the features dont work anymore.
I have windows XP home edition SP2
256MB Ram
20 GB Hard drive
1.2 ghz processor
I've left the xp_fix on the desktop just in case this ever happens again! It only took about 3 seconds - rebooted and WaLa! Have a great week 
Chowhound
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