I assume the dvd you're converting is a commercial dvd? In that case it's most likely encrypted. You'll need to decrypt the dvd first to your hard drive before running it through makemkv. I've always used dvdfab to do the decrypting. http://www.dvdfab.cn/hd-decrypter.htm
I read on this thread that we may have skipped a step. Try using the software "DVDFabHDDecrypter" and then extracting the audio from the decrypted iso/folder. Here is a link to the software (pretty sure it's freeware): http://www.dvdfab.cn/hd-decrypter.htm