www.makemkv.com

Tried to convert BlueRay ISO and received a pop-up complaing that AnyDVD was active. This pop up did not appear with any other type of ISO.
Disabled AnyDVD and restarted MakeMKV but still get the pop-up.

It's detecting that the ISO was created by AnyDVD. There is no need to pre-rip your disc, MakeMKV can handle them by itself.