11:51 a.m. on November 9, 2009 (EST)
As I commented in my 4-article series here on Trailspace and in various threads, backcountry water, whether spring, glacial melt, lake, stream, mud puddle, or whatever, may or may not be contaminated, and even if contaminated may or may not make you sick. Spring water usually is filtered by yards if not miles of the water travelling through soil, sand, and gravel, a technique that is used by many municipal water supplies.
Years ago, the Public Health Service (a federal government agency) recommended putting your outhouse about 100 yards from your well or the stream you got your water from (that was in the days when 70-80% of the US population was rural and most people had outhouses). This was thought to be sufficient filtering, and at a time when many outhouses were right on the banks of the creek (pronounced "crik" by most country folk in those days, and still in some parts of the country).
But there can be sources of pollution, including industrial and mine waste as well as biologics, in the path of the "filtering" flow.
You mention your "internal water purifier system". Depending on where you grew up, you developed resistance to a number of the local critters. I spent a good part of my childhood in rural areas, in the woods and hills (and desert) with my outdoorsy parents, and in Central America. As a result, I seem to have a lot of resistance to a lot of bugs. According to Paul Auerbach's huge Wilderness Medicine compendium (a several thousand page summary of articles on the subject, with an accompanying DVD that allows linking directly to the articles), a fair number of regular backcountry travellers are giardia carriers (analagous to the infamous Typhoid Mary, who was a cook in the late 19th Century who was immune to the typhoid she was carrying and passing along to the families for whom she worked).
The short answer to pburse, the OP, is that it is a combination of luck, plus the springs you have used not being contaminated, and maybe resistance you have built up. You cannot assure lack of contamination without thorough testing, which is impractical for the typical backcountry traveller.
Plus, giardiasis, crypto, and most of the other problem critters require an incubation period that often is a week or more. So you may pick up the bugs, but not be connecting the dots because you don't get sick until a week or more later.
Still, again according to the studies compiled by Auerbach, the main reason people get sick in the backcountry is not the contamination of the water, but carelessness in personal sanitation - as your mommy said, wash your hands, or at least use hand sanitizer religiously (or adopt the Middle Eastern custom of religiously designating your left hand as "unclean" and keeping your right hand as the "clean" hand)