Interesting. What water source were you using?
I thought my Steripen wasn't working once also.
I was filling my bottle straight out of a glacier. I pushed the button and put the UV bulb in the water, but it just blinked faintly a few times, and wouldn't turn on. I tried over and over. I even replaced the battery with my extra, but still no luck.
I cursed Steripens as junk and boiled water for the rest of the trip. When I got home I poured through the manual and found out that the UV Lamp won't work if it isn't submerged, as a safety feature. The sensor that tells the Steripen if it is submerged works by sensing the minerals in the water. IF the water you are trying to purify is too pure (like straight from a glacier) then there aren't any minerals to sense, and the Steripen thinks it isn't submerged, so it won't activate.
Of course, if the water is so pure the Steripen won't activate, it begs the question: Why purify at all?
However, just because the water is free of minerals doesn't mean some Pika didn't crap on the glacier, so I like to be sure.
Now I carry a little gas station packet of salt to mix in a pinch if the Steripen won't activate, but it hasn't happened again since.