just rattling some ideas around here for discussion purposes.
sounds to me like you got one of about three potential things going on (all minor variations of each other):
1) if it is all good clay.......because bottom or sides werent compacted, the water level gets to a certain height, and the hydraulic pressure becomes great enough to force water through yer pond sides or bottom but is slow enough to stay in ground downgradient of pond (hence you see no leakage).
2) maybe yer whole substrate really isnt clay. maybe you got a silt soil that the contractor didnt really identify. then same problem as above only a faster leak.
3) maybe you have a coarse grained layer (sand/gravel) only a couple feet below yer clay, and because of no compaction, the water found a pathway, gets in the coarse soil, migrates downgradient from pond but stays underground (hence you see no leaks).
if the leak can be determined as related to these types of problems, my truthful recommendation would be to drain, verify soil types, and compact, compact, compact.
anybody else?