Oh, I thought you found the source of the leak. Bummer. Those things can be hard to find.
In trying to locate the culprit, you might ask yourself how fast does the water escape? How many inches are lost within a certain period of time? If it's a lot, then it's probably a decent size hole which you should be able to locate by feeling around with your hand.
I guess you let it leak to the point where the leak stopped. As long as you are certain of this, you have most likely have nail it down to that level.
Are you sure it's not coming from any external hoses, piping, waterfall or skimmer? A large percentage of leaks develop around waterfalls.