Does the structure scan window have "no source found" or something similar? I have had similar issues with a loose Ethernet connection, the LSS-1 has power, but the cable was loose. After reconnecting the cable it will work. My loose connection is on the LSS-1, apparently we snag the cable and move it a little with our feet (it is under the passenger console).
The sonar uses a different transducer source than the side scan. That is why the sonar works, but not the side scan. Not sure about the downscan, it may use the sidescan transducer as well.
I know that you said the LSS-1 has the lights on it, so the switch should not be the issue. We have a separate power switch for the LSS-1, so I have to remember to turn that on or I have the same issue with no source.