J, not that John's wrong in that the liner needs to be protected from acidic water!, but how's the water table in your yard & equally important, what's the winter snow/ rainfall? It kind of sounds like the liner might have floated, leaving behind the wrinkles. It seems to me that a chemical problem would appear ~ evenly throughout the pool, while a 'ground water' issue would be primarily confined to the shallow end, where the pool water is less.