The 99.99% figure is the percentage of dives with no DCS. It is a rare event. The statistics include all dives, including those violating limits. I have heard that roughly half of DCS cases occur on dives on which the diver did not violate limits, meaning that the other half include violations. That means people following the limits are even less likely than those numbers indicate.
Here is a further complication--how do we know the people who were diagnosed with DCS actually had it? Many diagnoses are difficult, and they will frequently put the diver in the chamber when they are not sure. We had a thread a few years ago dealing with DAN's arguments with some chamber operators, and someone posted some documents related to it. In one interesting letter, DAN was talking about the need to have a properly trained physician making the diagnoses, because they believed many people who were being treated did not have DCS. They listed a number of maladies that are often misdiagnosed as DCS. Some of them not only present as DCS, the patient recovers in about the same amount of time someone would spend in the chamber, thus making it appear as if the chamber was the cure.