I can confirm that this is a bug. I checked the commits and I accidentially deleted this bit of code while formatting, directly after the commit that implemented Thorium Salt.
@Gregorius Just add the code bit into MultiTileEntityReactorCore1x1.java and MultiTileEntityReactorCore2x2.java, alongside the other fuels:
} else if (FL.Thorium_Salt.is(mTanks[0])) {
tEnergy = mEnergy / EU_PER_THORIUM_SALT;
if (mTanks[0].has(tEnergy) && mTanks[1].fillAll(FL.amount(MT.LiCl.mLiquid, tEnergy))) {
mEnergy -= EU_PER_THORIUM_SALT * mTanks[0].remove(tEnergy);
} else tIsExploding = T;