There was a previous thread (quite long) about this issue here in the "Newbies" forum. There were a number of suggestions and a few different solutions for the problem. Click on the link below and read all of the suggestions. One of them may work for you. Even the very last post in the thread worked for that individual.
Autoexec.nt Repair Thread
Hope this helps.
since removing a virus (amg free edition), my autoexec.nt file has been playing up.
I've looked at the knowledge base advice on microsoft.com and found how to expand this file from the original CD etc.
Whilst this works temporarily and avoids the "\system32\autoexec.nt 16 bit subsystem can't load some DOS or WINDOWS programs" error message, each time i re-boot I need to expand and reinstate the autoexec.nt file.
IS there a permanent fix anyone knows of?