I noted that when you dug your initial core trench you only went down 15 feet to the "ideal clay" soil. I am having a 5 acre lake built now and they dug down past the clay and hammered rock all the way down to the bedrock (about 3-4 feet of rock). They then brought clay back in the core and packed with a sheepfoot packer from the bedrock all the way up. They are still working on bringing dirt to the backside of damn and the lake is filling up and holding water almost too quickly.

If water is seeping down in your lake bottom through the soil/clay to the rock it could easily run under the core clay trench you have dug...

Maybe?

Good luck