thorium is not fully set up by bob's ores (and it isn't used for anything), so for now, i'd just say add it to the blacklist. that'll fix that issue, but not sure if that will prevent other issues with bob's ores, but definitely start there. just completely blacklist thorium. it isn't used for anything.
Unless you are like me and are using MadClown01's Nuclear Extension, which does use Thorium. Though even so, Thorium doesn't spawn as an ore itself, you get to it through research. I don't think the problem's related to Thorium only, though.
In the discussion I linked above, Kryzeth states:
All science packs are loaded into data.raw.tool (alongside the mining tools and repair packs, I think) as data.raw.tool["name-of-science-pack"], so you could easily scan that list, filter out the names with "science" in them, and use the resulting list of items to create liquid and liquid-to-solid recipes. This would allow you to support any mod that adds its own science packs, instead of just vanilla.
Haven't dived in to it myself, but there has to be a similar thing for ores, modded or vanilla.