The raised spa will never drain down below the level of the pool from a leak back into the pool that is why it stops were it does.
I assume the Return line you shut off with the 3-way valve is the one with the check valve. If true, then it sounds to me like the spa return check valve is leaking.
Hello , This thread has been inactive for over 60 days. New postings here are unlikely to be seen or responded to by other members. For better visibility, consider Starting A New Thread.
Welcome to TFP! For a wealth of pool care information please check out our free Pool School. If you are in need of specific help then we encourage you to Register and ask us here in the forum!