Sounds like some of the files from the old netboot weren't cleaned up properly while others were.
Check under /tftpboot/, there should be a subdirectory called pxelinux.cfg containing files named after the mac-adresses of the diskless MDs, I suspect that's where the problem lies. If you find them you could try moving the appropriate one out of the way by moving or renaming it. They are created automaticly when a new MD boots the first time.