I setup a job to mine silver and gold and I set to "as long as I have less than 3000 gold". This resulted in gold ore being mined, but the mod refused to flag the silver veins on the map for mining. It wasn't until I switched it to "less than 100,000 silver or gold" that it started actually flagging the silver veins.

Either there should be an option for "always flag this vein if available" option or you should be able to run with nothing selected in the counted set.