autoexec.nt and config.nt getting deleted?

There's an XP system running a DOS app which depends on the autoexec.nt and config.nt files within the Windows directory.

For some reason, these files keep getting deleted upon each reboot! I ended up writing a batch file, to place a copy of these files from a backup location into the right locations, to stop the system complaining that it couldn't find them.

Doesn't look like there are any startup programs or registry entries that are clearly deleting them, though I'm not excluding the possibility of some virus/malware.

Has anyone had this happen to them?

maybe this is a clue