Your skimmer should have come with a butterfly (sometimes called a "Wall Saver") gasket. It is U shaped in cross section. Half if it goes outside the wall and half inside, over the liner.
If this is installed correctly, and the skimmer faceplate is torqued down evenly, then you should not need silicone.
If your skimmer was leaking on the outside and you siliconed it, you have stopped the water from running down the outside of the pool. But have you stopped it from running down the wall behind the liner?
If you are reluctant to pull the whole thing apart (and I would be) you should also silicone the area between the simmer body and faceplate.