I think I fixed it. I don't have any "problem" DVDs here so I need some help testing. Test this on DVDs where the main movie is not track one. Also find a disk with at least one track that is LESS then one second. This seems to be what was causing the problem before. makemkv ignores these and doesn't even register them if minlength=0 is set.
avalx, Please update to the latest code and try to rip your DVD again. Then report the results.