OT: some computer help needed

[jdbubb at verizon.net (Dan Bubb)]

Dear List:

Cathy and I are pulling our hair out trying to get her engine running on Megasquirt.
It ran (idled) at one point, but now it will only try to run on one cylinder at best.
After trying everything Cathy, Drew or I could think of we believe the firmware in the Megasquirt CPU has become corrupted.

There is a batch file that is available for Megasquirt that downloads the firmware to the MS ECU.

When I run the batch file on my Windows XP laptop the Command Prompt window opens, prompts me for the comm port, then prompts me for the type of download I need to perform and then downloads the file giving status of the download once completed.

When Cathy tries to run the batch file on her Windows 2000 laptop the Command Prompt window opens but she also gets the following error in a separate error window that pops up and takes precedence over the Command Prompt window:

"16bit MS-DOS SUBSYSTEM
C:\WINNT\system32\cmd.exe
C:\WINNT\system32\autoexec.nt. The system file is not suitable for running
MS-DOS and Microsoft Windows applications. Choose 'Close' to terminate the
application.
Close/Ignore"

Choosing "ignore" causes the batch file to continue to the next prompt, but doesn't allow any entry in the Command Prompt window and then the error window opens again with the same message.

Ya know, it's just a lousy batch file for chrisake!

It sounds to me like one of the Microsoft files has a problem but what do I know?
Can anybody give any advice on how to overcome this? 

TIA
Dan