You see, when running water hits the still water, air gets mixed inside. So you get lotsa happy aerobic bacteria. (yes you have significantly less anaerobic bacteria)
So when they use the stuff, all your happy aerobic bacteria still alive and kicking, hook onto the apparatus and go into your coffee. Now our digestive system is anerobic in nature, and so when you insert aerobic bacteria, you upset the balance. Hence you get lotsa farts, churning in the stomach, cos these buggers just take up the carbon material which your anerobic bacteria is used to eating.
So at the end of the day, you just drink Vitagen or Yakult to re-balance your gut. Oh well, brings back memories of my micro-biology days when I used to daydream in lecture.