Interesting discussion. I've always heard the "wait a year" and let your pond settle out advice(and probably repeated it also), but my experience on ponds we've built is that they either leaked initially and the leaks didn't stop until repaired or they didn't leak at all, at least noticeably or unacceptably. Leaks can be confused with absorption, which I've also experienced. In ponds I've built, we always use some of the sandy soils above the clay layers to create underwater structures, submerged islands, etc. These areas, in dry conditions, can absorb considerable water as the pond fills...but that effect is short term in my experience.
Don, if I had a 1/2 inch per day water loss this time of year, I would be concerned and trying to find any evidence of where the water may be going. Seems to me that most of your absorption would have been satisfied with the two 3 inch rains you mentioned. On the other hand, other than look very carefully for water evidence, and without finding any evidence, I wouldn't take any drastic steps. I would give it some time and carefully measure true loss rates to discern if indeed, the loss rates are decreasing. If they aren't decreasing after a couple of months, then I'd be after my contractor for action.
