This happened to me as well, but I was able to work around it using work orders through the manager. This is known to also happen with soap makers.
In case you aren't familiar...
Assign a "manager" noble and give him a study (assigned through a chair).
hit j->m and narrow the tasks list by typing the order you desire. Select the one you want with +/-, and enter a quantity.
For example, when I want to pump out a batch of Steel bars using flux, iron, and magma forges. I order "Make charcoal" x30, "Smelt pig iron bars" x15 and then "smelt steel bars" x15 (this actually produces 30 bars, because steel is produced 2 bars at a time). The great thing about work orders is that...
1) Job cancellations won't change their set quantity, so you can set them and forget them instead of having to wait for the first product (pig iron) to be done before ordering the second (steel). As the pig iron bars roll out, jobs to turn them into steel will queue up automatically, and if no more pig iron is available to make steel, the orders to smelt steel will be removed until some is available.
2) If you are like me, you probably have smelters set to "smelt (some ore) /R." Work orders for smelting will jump ahead of these smelting orders, but will leave them in place when the work order is done with no micro-management required, so you can get right back to pumping out iron bars to start the process over again without even having to look at your smelter(s).
This is REALLY useful for a certain spoiler-related metal, as it will allow you to turn strands into bars without giving the time for other dwarves (i.e. hospital) to waste the precious threads on mundane tasks.
I get a lot of mileage out of my manager. Much more than his "meager office" would suggest.