Most likly your problem is caused by moisture from your air collecting on the parts of the ceiling where there is no insulation. Joists do no have the R-value of regular insulation and therefor the ceiling and walls will be colder where the joist and studs are. These moister areas will then be able to collect soot and other particles from the air much easier than the rest of the area. If you look closely, you may also be able to see where th screws or nails are that hold up the drywall. You could try to wash them, but most likely, you'll have to repaint, using a stain killing primer. An easy stain killing primer is Brunning's "Grabber Plus". It's latex and even though I don't place much faith in most latex stain killers, this one really works well.