If 5.3-5.4 is pH at mash temperature, it's in the right range. If that's a room temperature sample's pH, then it's low, and could account for the problems you find in the beer, IME. A bit more alkalinity in the water could bring your mash pH up to the more appropriate range, approaching 5.6 (room temperature,) which could help improve body and flavor, as well as extract and more.
As for what you're experiencing adding it to the glass, I'm not so sure. You might try searching the forum for posts on this by dmtaylor. I recall he has some considerable experience in correcting dark beers after the fact with bicarbonate.