We had some serious ice dam issues last year so they were water spots. This happens every few years depending on how much snow we get and when. I've always used the oil-based spray cans (Kilz or Zinsser) and they cover like magic. I expect the problem was trying to cover water spots with a water-based sealer.
I contacted the Kilz people and they offered to replace my quart of the latex with a gallon of the oil, but it wasn't worth jumping through all their hoops (pictures of the can, the spots and receipts, etc). I did find an old spray can of Kilz in the basement and it covered in one coat. I suspect that any brand of latex sealer may have trouble with water spots. I'll stick with oil in the future.
dss