You are correct sir (or ma'am), I was referring to the copper / tin / silver / etc. blocks that spawn as ID 2001, which are from thermal expansion (I had thought they were GT for some reason). Another example is AE's quartz (2512). I could probably just add them manually easily enough, but I don't know what other things I'd be missing out on unless I went through NEI ore by ore and made a list, compared to a BC Quarry or Frame miner which will get all ores no matter what.
Has anyone used an IC2 miner and bothered to make a complete listing of the S:valuableOres config for the FTB Ultimate pack?
Unfortunately this leaves IC2 miners at a severe disadvantage to other mining systems, even compared to manual mining, unless you make a list and edit the config. If you're playing on a server and can't change the configs, they're basically not an option. I hope the FTB team can set the default config to account for this in the future.