Mark, did you take a "diary" of pics during construction? Perhaps if you had a few during initial stages, some of the experts here could evaluate how and if you dam was cored (built w/ a keyway) which in turn might eliminate some seepage possibilities/theories.
I have a "bedrock" pond built over a seasonal creek bed as well. Prior to renovation, the pond would fill, and stay full, in rainy season. After rains quit, it would rapidly drain out to a certain level, then evaporate the rest of the way. at first i thought it a dam problem, but realized it was hydraulic head (depth of water) exerted on the bedrock substrate. water was driven through fractures and daylighting just downstream of dam. my only affordable fix was to import clay, and combine with native clay i had on property to seal particularly the deepest parts of pond (where hyd. head was greatest). now 8-mos. post renovation, the pond is holding more water than it has in over 10 years, albeit evaporating alot more than i want, but creek is dry downstream of pond......the type of bedrock we have here weathers in such a way that clays dominate the fracture zones, however, in the creek bed, the bedrock was much less weathered, and fractures void of clays......which is where it seeped.......not along the sides in the weathered bedrock, but in the creek channel in the fresh bedrock.
i dont know if any of this helps, but perhaps sharing a similar "bedrock" pond story may spur some ideas.
