I think the problem here is one of 2 things.
The Catch pool is improperly sized, when you shut off the negative edge pump the water overflows the catch basin and goes out the drain that should be there. The water that overflows the catch basin is the water that is on top of the weir (negative edge) usually about 1/8".
If water evaporates the water will still retain the salt.
To rectify the situation you will need to either look into raising the overflow level, and/or lowering the autofill level.
When you tested for leaks, did you have the negative edge pump running? Its possible that there is a leak in the negative edge return line, or possibly even water falling off the weir, or wall.
You can try running the edge pump with the autofill off, but make sure you are around during this test. You can also put a water meter in the autofill line to track how much water the pool is using (never a bad idea with this type of pool).