The default config file has the tags for lapis, gold, and diamond ores missing from both the ores tags. I'm not sure if that is why it didn't detect them, but I had to use a block module with gold ores in it before the scanner would detect the ore.

scannable-common config.zip
here's both the default config, and my edit to make it include those three ores

Emerald ores were missing too.

All ores (based on the ores tag, c:ores) not listed in common should automatically picked up by the rare ore scanner.

Are these blocks missing that tag?

I don't know how to check that, but I do know the scanner tool wasn't detecting them until I manually added them in.