This may happen if bars are stored in bins and the bins get carried around to collect bars from the smelter, thus making them currently unavailable.
It shouldn't though, as I have a ton of bins and bars just laying around, none of them having hauling jobs assigned to them : \
I have a rather huge stockpile of pig iron and coke for one smelter, and plenty of flux and hematite, but for some reason it won't let me smelt anything but coal into coke suddenly.
EDIT - Now it will smelt the iron ores i have, but still a no for pig iron or steel.
Are _iron_ bars allowed on the stockpiles? The ingredients for the smelter reaction are one carbon, one pig iron, one flux stone and one iron bar. If any one of them is missing, the whole reaction doesn't work, and if one's missing on the linked stockpiles, the reaction cannot be ordered at the smelter. It can be _performed_ if there are iron bars inside the smelter itself, but adding the order from the 'q'uery list is not possible. At least that was my experience.
I usually just place the relevant stockpiles nearby and leave the steel-cooker unlinked. That sometimes backfires (when a dwarf decides to grab a limestone boulder at the surface and then slooooooooooowly drags it down a hundred stairs), but usually works alright.
That might be the case, I rooted around and couldn't find any.
Another problem came up though - Even though I have a ton of hematite and limonite available, it's telling me none exist, though all are not forbiddendumped, and are just sitting on my stockpile for them.
EDIT - Found out the problem, apparently the smelter would ONLY make use of the ore if the stockpile was set to the smelter. Thank you all for the help though!