BigPond, hello old friend. I see you have finally made the discovery of why your pond is not filling up. I hate to hear it, for sure, and assumed by your prior posts, that there was so much clay you wouldn't have to worry about it.
The good news, is just that, you do have lots of clay to work with. If you can not determine where the water is going through, and the only way I can think of, if it is not just obvious, is by witching the void, then you will need to treat the entire floor above the water line with a clay blanket, to be sure, or lesser measures of disking and compacting and or hogs sealing your clay.
Good luck, and though I'm not around as much these days, I have noted your absence.
One last thought, be sure to look at all of your photos during lake construction. A problem I have personally had, is from stump holes that I had forgotten about creating, upon removal of various trees.
