First, since the liner was put in only 2 weeks ago, get the installer back. Quite possibly he overlooked something like tightening all the pinch strips on the stairs. That would be simple. Just because it didn't seem to leak immediately doesn't let him off the hook in my opinion. If the liner was stressed during install maybe a seam let go or maybe a thin spot in the liner did the same. From what you said the skimmer is not the problem. If the water is still above the returns, plug them.
Al