I am getting an eror message as soon as i choose N64 in the list, not after scanning. I can't even get to the scanning part. Does anyone have any idea what the cause is and how to fix it?
Do you get the same result if you run the Goodtool app from a command line, or if you use a different frontend such as GoodWork? Clear out any generated have/miss/dupe lists in the rom folders as well.