You are getting errors referring to the inability to run 16-bit programs, or an error similar to:
The system file is not suitable for running MS-DOS and Microsoft Windows applications. Choose 'Close' to terminate the application.
Similar to the CONFIG.SYS and AUTOEXEC.BAT files for DOS and Windows 9x, CONFIG.NT and AUTOEXEC.NT establish a runtime environment to support CD-ROM drives, network redirection, sound, and mouse features for DOS and 16-bit applications running under Windows XP. For no good reason it seems one or both of these files can mysteriously disappear due to a recent software installation or disk fault. The cure is simple if only the error message made more sense.
Scouring the Web and Microsoft's site turn up no clues as to how or why the AUTOEXEC.NT or CONFIG.NT files disappear and cause these errors, as http://www.annoyances.org/exec/forum/win2000/1106422202 and other help forums indicate frequently.