Cyclone III vs USB Blaster Rev. B

I work for a contract manufacturer, I am programming and testing hundreds of boards, and I use a shell file created by our customer and NIOS shell. The errors that I've seen range from minor failures like a bad A to D reading or the eithernet port not communicating properly to the unit under test behaving as if it hadn't been programmed at all. How it can "sort of" program a unit, I'll never know. Since I've gotten the Rev C USB Blaster, I've programmed exactly 99 units with no errors.