If I remember correctly, you'll also see that message if the source material you are using was in any way created or modified by AnyDVD (ripped, copied, backed up). If using such modified source material does, in fact, result in an error, just re-rip your original, commercial BluRay disc with ONLY makeMKV (and with AnyDVD COMPLETELY turned off)...
I see what you mean... I had a movie decrypted here tested and MakeMKV crashed twice after that warning, that was not given in another case. At first I thought AnyDVD was somehow activated without my knowledge, but what this warning really indicates is what you explained to me.
Still don't know what the problem is, though. Wrong choices while decrypting? Or simply incompatibility with AnyDVD and the files created? Anyway, this warning message is confusing... it should have stated what you told me to do.
Perhaps the wording of the message could be a bit more clear but, regardless, just be aware that there have been postings at many forums, indicating that problems have resulted from using AnyDVD (or other similar programs) in conjunction with makeMKV (Whether at the same time or separately with regard to the same title.
Therefore, if you use only original, commercial Blu-rays and DVDs together with MakeMKV, you won't run the risk of inadvertently fouling up your effort...