As a quick check to see if it is the soil or a hole, give the soil a bucket test. Search the forums for more info, but I believe you take a 5-gallon bucket, drill in a bunch of holes in the bottom. Add soil from pond bottom to the bucket about half-way, and compact somehow. Pour in water and see if anything comes out of the bottom.
I would be curious to see if the soil leaks in this test, and even more curious to see if adding water softener salt to the bucket would make any difference if it does leak.
I tried this, but my initial test didn't leak so I couldn't test the softener salt idea. The theory is ion exchange in the clay allows it to go from granular clumpy clay bits to slick mushy clay that plugs well.
