It was supposed to mean 99.xxx% Good parts exiting the building. But yeah, it's like Organic and Range Free. I used to do work for Boeing and other Aerospace MFGs and they would have the Inspectors come in from those Orgs and 100% inspect every pc...
Like any other manufacturing of anything, there is always a level of quality issues. Unless a company is ISO9000 like, there will always be defective items sold. Take a look at Boeing, and they are ISO 9000 certified.