Are you missing some .R00, .R01, .R02, etc. files? You need to include these files for RAW2DNG to be able to convert your files (The RAW format uses a "footer" to store the info it needs to be able to properly convert the files, this is only at the end of the very last file, so if you are missing the last file or it is corrupted, it wont convert. The MLV format is a more robust format that alleviates potential issues like this by including metadata in every chunk file, and so I highly recommend using it instead).
ML automatically splits files when they reach 4GB b/c some filesystems don't support files larger than 4GB. Once 4GB is reached, ML will start writing into .R00, and so on and so forth.