I've had a few occurrences now in which my breathing counter has stopped ticking down whilst underwater. I haven't observed any particular trends, though when it happened this time, it stopped ticking after I used a scroll of Endurance on my PC while underwater.
Possible the feedback got lost in your combat log. There could stand to be feedback at every 15 second interval instead of 30 seconds as it currently is.
On this occurrence, there was no combat for a period of nearly fifteen minutes after casting endurance, right up until the end of the DM event in which I was underwater. I had no need for using lungroots, and each time I tried it told me that my lungs were full.